satarupa22/MacromolecularLigandDB huggingface dataset:
Human PDK1 Kinase Domain in Complex with Adenine Bound to the ATP-Binding Site (PDB entry 5LVM)
Macromolecule: 3-phosphoinositide-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: GAMDGTAAEPRPGAGSLQHAQPPPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.26
R work: 0.1335
R free: 0.1549
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, 10 MM DTT
Matthews coefficient: 2.13
Solvent content (%): 42.35
Ligand: DITHIANE DIOL (DTD)
Ligand formula: C4 H8 O2 S2
Ligand molecular weight: 152.235
Ligand SMILES: C1C(C(CSS1)O)O
Ligand InChI: InChI=1S/C4H8O2S2/c5-3-1-7-8-2-4(3)6/h3-6H,1-2H2/t3-,4-/m0/s1
Release date: 2016-10-19
Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a double methylated Fasudil-derivative (PDB entry 5M6V)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Cricetulus griseus
EC number: 2.7.11.11
Sequence length: 353 residues
Sequence: GHMGNAAAAKKGSEQESVKEFLAKAKEEFLKKWESPSQNTAQLDHFDRIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.418
R work: 0.1435
R free: 0.174
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 277.15
Crystal growth procedure: Drop:
10 mg/ml PKA (0.240 mM)
30 mM MBT (MES/Bis-Tris Puffer pH 6.9)
1 mM DTT
0.1 mM EDTA
75 mM LiCl
0.03 mM Mega 8
0.07mM PKI (Sigma: P7739)
1.2 mM ligand solved in DMSO (50 mM Stock)

Reservoir: 18% Methanol

0.003 mL drop volume, 0.4 mL reservoir volume
Matthews coefficient: 2.15
Solvent content (%): 54.27
Ligand: (S)-2-METHYL-1-[(4-METHYL-5-ISOQUINOLINE)SULFONYL]-HOMOPIPERAZINE (H52)
Ligand formula: C16 H21 N3 O2 S
Ligand molecular weight: 319.422
Ligand SMILES: Cc1cncc2c1c(ccc2)S(=O)(=O)N3CCCNCC3C
Ligand InChI: InChI=1S/C16H21N3O2S/c1-12-9-18-11-14-5-3-6-15(16(12)14)22(20,21)19-8-4-7-17-10-13(19)2/h3,5-6,9,11,13,17H,4,7-8,10H2,1-2H3/t13-/m0/s1
Release date: 2018-06-06
The co-structure of N,N-dimethyl-4-[(6R)-6-methyl-5-(1H-pyrrolo[2,3- b]pyridin-4-yl)-4,5,6,7-tetrahydropyrazolo[1,5- a]pyrazin-3-yl]benzenesulfonamide and a rationally designed PI3K-alpha mutant that mimics ATR (PDB entry 5UKJ)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 1074 residues
Sequence: MPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSKKLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECEIMSSAKRPLKLNWENPDIMSELLFQNNIIMFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEWVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLVHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIFHTIKQHALNHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.187
R free: 0.252
Average B factor: 63.17
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 303.15
Crystal growth procedure: 3 UL OF PROTEIN WAS MIXED WITH 5 UL OF WELL SOLUTION CONTAINING 12% PEG 3350 AND 120 MM POTASSIUM  THIOCYANATE, PH 7.2, VAPOR DIFFUSION, HANGING DROP,
Matthews coefficient: 2.33
Solvent content (%): 47.13
Ligand: N,N-dimethyl-4-[(6R)-6-methyl-5-(1H-pyrrolo[2,3-b]pyridin-4-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-3-yl]benzenesulfonamide (3K6)
Ligand formula: C22 H24 N6 O2 S
Ligand molecular weight: 436.53
Ligand SMILES: CC1Cn2c(c(cn2)c3ccc(cc3)S(=O)(=O)N(C)C)CN1c4ccnc5c4cc[nH]5
Ligand InChI: InChI=1S/C22H24N6O2S/c1-15-13-28-21(14-27(15)20-9-11-24-22-18(20)8-10-23-22)19(12-25-28)16-4-6-17(7-5-16)31(29,30)26(2)3/h4-12,15H,13-14H2,1-3H3,(H,23,24)/t15-/m1/s1
Release date: 2017-05-10
Human GAR transformylase in complex with GAR substrate and AGF132 inhibitor (PDB entry 8FDY)
Macromolecule: Phosphoribosylglycinamide formyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.2.2
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.2106
R free: 0.255
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris-HCl pH 7.5, 0.33 M NaCl, 16-21% PEG 4000, and 2% PEG 400
Matthews coefficient: 3.56
Solvent content (%): 65.4
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2023-05-10
Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9l (PDB entry 5N67)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1895
R free: 0.222
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.2
20-30 % PEG4000
50 mM BOG
Matthews coefficient: 2.35
Solvent content (%): 47.61
Ligand: 1-[4-[4-[7-azanyl-4-(2-phenylethylamino)quinazolin-2-yl]phenyl]piperazin-1-yl]ethanone (8ON)
Ligand formula: C28 H30 N6 O
Ligand molecular weight: 466.577
Ligand SMILES: CC(=O)N1CCN(CC1)c2ccc(cc2)c3nc4cc(ccc4c(n3)NCCc5ccccc5)N
Ligand InChI: InChI=1S/C28H30N6O/c1-20(35)33-15-17-34(18-16-33)24-10-7-22(8-11-24)27-31-26-19-23(29)9-12-25(26)28(32-27)30-14-13-21-5-3-2-4-6-21/h2-12,19H,13-18,29H2,1H3,(H,30,31,32)
Release date: 2017-09-20
Structure of human SIRT2 in complex with 1,2,4-Oxadiazole inhibitor and ADP ribose. (PDB entry 5MAR)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 303 residues
Sequence: HMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.1732
R free: 0.1943
Average B factor: 38.23
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 293
Crystal growth procedure: 15-18 % PEG 10,000, 0.1M ammonium acetate, and 0.1M Bis-Tris pH 5.8
Matthews coefficient: 2.45
Solvent content (%): 49.74
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-03-15
Human Sirt6 in complex with ADP-ribose and fragment nicotinamide (PDB entry 8AKE)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1767
R free: 0.2237
Average B factor: 35.089
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.6
Solvent content (%): 52.79
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2023-08-16
Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin (PDB entry 6TUV)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase MINDY-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 289 residues
Sequence: GPLGSPEFPGRLEMEPDFYCVKWIPWKGEQTPIITQSTNGPAPLLAIMNILFLQWKVKLPPQKEVITSDELMAHLGNCLLSIKPQEKSEGLQLNFQQNVDDAMTVLPKLATGLDVNVRFTGVSDFEYTPECSVFDLLGIPLYHGWLVDPQSPEAVRAVGKLSYNQLVERIITCKHSSDTNLVTEGLIAEQFLETTAAQLTYHGLCELTAAAKEGELSVFFRNNHFSTMTKHKSHLYLLVTDQGFLQEEQVVWESLHNVDGDSCFCDSDFHLSHSLGKGPGAEGGSGSPE
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.2075
R free: 0.249
Average B factor: 49.244
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM Tris-HCl, 200mM LiSO4.H2O, 30% PEG400
Matthews coefficient: 2.4
Solvent content (%): 48.67
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2021-01-27
Human JMJD5 in complex with MN and 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid. (PDB entry 7DYW)
Macromolecule: Bifunctional peptidase and arginyl-hydroxylase JMJD5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 236 residues
Sequence: QSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.2142
R free: 0.2392
Average B factor: 53.09
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride
Matthews coefficient: 2.36
Solvent content (%): 47.84
Ligand: 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid (HRL)
Ligand formula: C15 H14 N2 O5
Ligand molecular weight: 302.282
Ligand SMILES: COc1ccccc1CNc2cnc(cc2C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C15H14N2O5/c1-22-13-5-3-2-4-9(13)7-16-12-8-17-11(15(20)21)6-10(12)14(18)19/h2-6,8,16H,7H2,1H3,(H,18,19)(H,20,21)
Release date: 2022-02-02
DNA Polymerase Mu (K438D), 8-oxodGTP:Ct Ground State Ternary Complex, 50 mM Mg2+ (90min) (PDB entry 7KTK)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSDLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.419
R work: 0.1428
R free: 0.1684
Average B factor: 24.598
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.43
Solvent content (%): 49.35
Ligand: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (8DG)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(27-5)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
Release date: 2022-05-11
Crystal structure of GSDMB in complex with Ipah7.8 (PDB entry 7WJQ)
Macromolecule: Probable E3 ubiquitin-protein ligase ipaH7.8
Type: Protein, polypeptide(L)
Source organism: Shigella flexneri
EC number: 2.3.2.27
Sequence length: 242 residues
Sequence: SNEHYLRILTEWEKNSSPGEERGIAFNRLSQCFQNQEAVLNLSDLNLTSLPELPKHISALIVENNKLTSLPKLPAFLKELNADNNRLSVIPELPESLTTLSVRSNQLENLPVLPNHLTSLFVENNRLYNLPALPEKLKFLHVYYNRLTTLPDLPDKLEILCAQRNNLVTFPQFSDRNNIRQKEYYFHFNQITTLPESFSQLDSSYRINISGNPLSTRVLQSLQRLTSSPDYHGPQIYFSDSD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2102
R free: 0.2522
Average B factor: 53.35
Crystallization method: LIQUID DIFFUSION
Crystallization temperature (K): 291.15
Crystal growth procedure: NaCl, HEPES sodium, PEG 8000, ammonium sulfate, 1,6-hexanediol
Matthews coefficient: 2.19
Solvent content (%): 43.86
Release date: 2023-01-11
Crystal structures and ribonuclease activity of the Flavivirus host factor ERI3 that is involved in viral RNA synthesis define the ERI subfamily of structure-specific 3-prime - 5-prime exoribonucleases (PDB entry 7K05)
Macromolecule: ERI1 exoribonuclease 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 216 residues
Sequence: MHHHHHHENLYFQSMSFPPQRYHYFLVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGFIFKQTSKPF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1715
R free: 0.2117
Average B factor: 50.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 290
Crystal growth procedure: 30% MPEG 2K,
20% saturated KCl,
200 mM pH 8.4 Imidazole / Malate
Matthews coefficient: 2.1
Solvent content (%): 41.31
Ligand: ADENOSINE MONOPHOSPHATE (AMP)
Ligand formula: C10 H14 N5 O7 P
Ligand molecular weight: 347.221
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2021-10-06
STX-478, a Mutant-Selective, Allosteric Inhibitor bound to H1047R PI3Kalpha (PDB entry 8TGD)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.137
Sequence length: 1068 residues
Sequence: MPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDARHGGWTTKMDWIFHTIKQHALN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.928
R work: 0.2175
R free: 0.2516
Average B factor: 132.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.5 M NaCl, 0.1 M MES-NaOH pH 6.8, 5% w/v PEG 3350
Matthews coefficient: 2.98
Solvent content (%): 58.74
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2023-09-06
Structure of DHODH in Complex with Ligand 17 (PDB entry 8VHL)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 369 residues
Sequence: GAMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.16764
R free: 0.19903
Average B factor: 22.087
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 4.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M NaAcetat_pH4,8 2.30 M (NH4)2SO4 30 % Glycerol, 18% (w/v) PEG 4000, 0,1M Na3Citrate pH=5.75
Matthews coefficient: 3.55
Solvent content (%): 65.39
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2024-04-03
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with beta-gamma difluoro analogue of dGTP (PDB entry 6NKT)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEMGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1994
R free: 0.3027
Average B factor: 51.6866
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.48
Solvent content (%): 50.42
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-01-08
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4,6-tetrakisphosphate/ADP/Mn after reaction (PDB entry 8PPG)
Macromolecule: Inositol-trisphosphate 3-kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.127
Sequence length: 279 residues
Sequence: GSHMSWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.206
R free: 0.2435
Average B factor: 44.186
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. 
Protein:precipitant ratio 1:1. 
Protein concentration: 17 mg/ml. 
Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. 
Soaking overnight with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 7 mM beta-D-glucopyranosyl 1,3,4-trisphosphate (substrate), 10 mM ATP and 10 mM MnCl2.
Matthews coefficient: 2.63
Solvent content (%): 53.23
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2024-02-28
Crystal structure of EED [G255D] in complex with EZH2 peptide and EED226 compound (PDB entry 5WUK)
Macromolecule: Polycomb protein EED
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 366 residues
Sequence: KKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCDMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.16
R free: 0.191
Average B factor: 27.7
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 10% polyethylene glycol (PEG) 6000, 0.1M Bicine(pH9.0)
Matthews coefficient: 2.52
Solvent content (%): 51.15
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2017-05-03