satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of phosphorylated p38aMAPK in complex with TAB1 (PDB entry 5NZZ)
Macromolecule: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 504 residues
Sequence: MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSENNCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLESIDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYVANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQESTRRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAHGPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTLLVRNFGYPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNGAHSASTLDEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2187
R free: 0.2707
Average B factor: 61.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG3350, 0.1M magensium chloride, 0.1M magnesium sulphate, 0.1M Tris pH8.5
Matthews coefficient: 3.06
Solvent content (%): 59.83
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2018-05-30
Crystal structure of human carbonic anhydrase II with N-((1-(6-((3aR,7R,7aS)-7-hydroxy-2,2-dimethyltetrahydro-[1,3]dioxolo[4,5-c]pyridin-5(4H)-yl)hexyl)-1H-1,2,3-triazol-4-yl)methyl)-4-sulfamoylbenzamide (PDB entry 7NH8)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.369
R work: 0.1618
R free: 0.1899
Average B factor: 17.412
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.13
Solvent content (%): 42.35
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: 2022-02-23
HRAS R97M Crystal Form 1 (PDB entry 8ELZ)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 189 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYMEQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.961
R work: 0.1565
R free: 0.202
Average B factor: 28.5357
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: PEG 3350,
Calcium Acetate,
Magnesium Chloride,
Sodium Chloride,
DTT
Matthews coefficient: 2.43
Solvent content (%): 49.4
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2023-09-06
Crystal structure of Ago2 MID domain in complex with 6-(3-(2-carboxyethyl)phenyl)purine riboside monophosphate (PDB entry 7C6B)
Macromolecule: Protein argonaute-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26
Sequence length: 139 residues
Sequence: KQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNIL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1944
R free: 0.2286
Average B factor: 42.944
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1M imidazole pH8.0, 0.2M NaCl, 0.46M NaH2PO4, 1.84M K2HPO4
Matthews coefficient: 2.6
Solvent content (%): 52.74
Ligand: 3-[3-[9-[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid (K2R)
Ligand formula: C19 H21 N4 O9 P
Ligand molecular weight: 480.365
Ligand SMILES: c1cc(cc(c1)c2c3c(ncn2)n(cn3)C4C(C(C(O4)COP(=O)(O)O)O)O)CCC(=O)O
Ligand InChI: InChI=1S/C19H21N4O9P/c24-13(25)5-4-10-2-1-3-11(6-10)14-15-18(21-8-20-14)23(9-22-15)19-17(27)16(26)12(32-19)7-31-33(28,29)30/h1-3,6,8-9,12,16-17,19,26-27H,4-5,7H2,(H,24,25)(H2,28,29,30)/t12-,16-,17-,19-/m1/s1
Release date: 2020-11-25
HsMetAP in complex with (1-amino-2-propylpentyl)phosphonic acid (PDB entry 4U1B)
Macromolecule: Methionine aminopeptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 306 residues
Sequence: YRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCYPSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHGDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHAQANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARPHFMSQF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.169
R free: 0.221
Average B factor: 33.14
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: PEG 2000, potassium chloride, hepes, sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Matthews coefficient: 2.47
Solvent content (%): 50.29
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: 2015-03-25
Crystal structure of Tdp1 catalytic domain in complex with compound XZ515 (PDB entry 6DJH)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.918
R work: 0.1773
R free: 0.2303
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03M sodium fluoride
0.03M sodium bromide
0.03M sodium iodide
Matthews coefficient: 2.46
Solvent content (%): 49.9
Ligand: 8-bromo-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (GNM)
Ligand formula: C10 H6 Br N O3
Ligand molecular weight: 268.064
Ligand SMILES: c1cc2c(c(c1)Br)NC=C(C2=O)C(=O)O
Ligand InChI: InChI=1S/C10H6BrNO3/c11-7-3-1-2-5-8(7)12-4-6(9(5)13)10(14)15/h1-4H,(H,12,13)(H,14,15)
Release date: 2019-05-29
Complex between MTH1 and compound 29 (a 4-amino-2,7-diazaindole derivative) (PDB entry 6F22)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.16941
R free: 0.20546
Average B factor: 18.783
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 22% PEG4K, 0.24M AmSO4, 12.5% glycerol
Matthews coefficient: 2.25
Solvent content (%): 45.43
Ligand: (3~{S})-3-phenyl-4-(2~{H}-pyrazolo[3,4-b]pyridin-4-yl)morpholine (C9B)
Ligand formula: C16 H16 N4 O
Ligand molecular weight: 280.324
Ligand SMILES: c1ccc(cc1)C2COCCN2c3ccnc4c3c[nH]n4
Ligand InChI: InChI=1S/C16H16N4O/c1-2-4-12(5-3-1)15-11-21-9-8-20(15)14-6-7-17-16-13(14)10-18-19-16/h1-7,10,15H,8-9,11H2,(H,17,18,19)/t15-/m1/s1
Release date: 2018-03-07
PanDDA analysis group deposition -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000299a (PDB entry 5QHV)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 183 residues
Sequence: SMFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSNSFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIHVIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDAIEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKREG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.05
R work: 0.2029
R free: 0.2179
Average B factor: 13.855
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 80 mM KBr, 30 % PEG2kMME
Matthews coefficient: 1.99
Solvent content (%): 38.19
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2019-04-10
Crystal structure of 1-hydroxy-5-(trifluoromethyl)pyridine-2(1H)-thione bound to human carbonic anhydrase II (PDB entry 4Q8X)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.16336
R free: 0.20077
Average B factor: 10.955
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 2.07
Solvent content (%): 40.51
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: 2015-03-11
Crystal structure of anti-HER2 antibody H2Mab-119 in complex with HER2 domain I (PDB entry 8JYR)
Macromolecule: Receptor tyrosine-protein kinase erbB-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 202 residues
Sequence: TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTASHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1734
R free: 0.2087
Average B factor: 38.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Sodium citrate pH5.5, 20% w/v PEG3000
Matthews coefficient: 2.63
Solvent content (%): 53.19
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2024-03-13
Crystal structure of Casein Kinase I delta (CK1d) in complex with monophosphorylated p63 PAD1P peptide (PDB entry 6RU6)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 296 residues
Sequence: SMMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2108
R free: 0.257
Average B factor: 50.924
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 10-20% PEG 3350, 0.1-0.2 M sodium sulfate and 0.1 M citrate, pH 4.6-5.9
Matthews coefficient: 2.4
Solvent content (%): 48.77
Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER (ACP)
Ligand formula: C11 H18 N5 O12 P3
Ligand molecular weight: 505.208
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
Release date: 2020-05-13
Crystal structure of autotaxin gamma in complex with LPA 18:1 (PDB entry 8C3P)
Macromolecule: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.39
Sequence length: 888 residues
Sequence: MARRSSFQSCQIISLFTFAVGVNICLGFTAHRIKRAEGWEEGPPTVLSDSPWTAISGSCKGRCFELQEAGPPDCRCDNLCKSYTSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLARGDCCTNYQVVCKGESHWVDDDCEEIKAAECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHSPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVKAGTFFWSVVIPHERRILTILQWLTLPDHERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKIVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRSKFSNNAKYDPKAIIAALTCKKPDQHFKPYLKQHLPKRLHYANNRRIEDIHLLVERRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGSTFKYKTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPEEVTRPNYPGIMYLQSDFDLGCTCDDKVEPKNKLDELNKRLHTKGSTEAETRKFRGSRNENKENINGNFEPRKERHLLYGRPAVLYRTRYDILYHTDFESGYSEIFLMPLWTSYTVSKQAEVSSVPDHLTSCVRPDVRVSPSFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWNYFQRVLVKKYASERNGVNVISGPIFDYDYDGLHDTEDKIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNEESCNSSEDESKWVEELMKMHTARVRDIEHLTSLDFFRKTSRSYPEILTLKTYLHTYESEI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.2221
R free: 0.28
Average B factor: 42.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 18-22 % PEG 3350, 0,1-0,4 M Ammonium Iodide, 0,1-0,4 M Sodium Thiocyanate
Matthews coefficient: 2.18
Solvent content (%): 43.45
Ligand: 7alpha-hydroxycholesterol (5JK)
Ligand formula: C27 H46 O2
Ligand molecular weight: 402.653
Ligand SMILES: CC(C)CCCC(C)C1CCC2C1(CCC3C2C(C=C4C3(CCC(C4)O)C)O)C
Ligand InChI: InChI=1S/C27H46O2/c1-17(2)7-6-8-18(3)21-9-10-22-25-23(12-14-27(21,22)5)26(4)13-11-20(28)15-19(26)16-24(25)29/h16-18,20-25,28-29H,6-15H2,1-5H3/t18-,20+,21-,22+,23+,24-,25+,26+,27-/m1/s1
Release date: 2023-11-22
Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A (PDB entry 5HQ8)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 432 residues
Sequence: GSFTMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.1741
R free: 0.2011
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 295
Crystal growth procedure: Human SMYD3 (1-428) with SAM in the SAM-binding site was concentrated to 11.7 mg/mL in 25 mM Tris-HCl pH 8 and 150 mM NaCl.  Peptide (21st Century Biochemical) was solubilized in 100mM water.   Two ul peptide was added to 200 ul of protein (five fold molar excess of peptide) and allowed to complex with the protein overnight at 4C.  Crystals were obtained from a Hampton Index HT broad screen in sitting drops at 22C with condition H7 (0.15 DL-malic acid pH 7.0, 20% w/v PEG 3,350).   Crystals were flash frozen in 20 percent ethylene glycol in well  solution prior to data collection
Matthews coefficient: 2.63
Solvent content (%): 53.28
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: 2016-03-30
Crystal structure of mouse MUTYH in complex with DNA containing AP site analogue:8-oxoG (Form I) (PDB entry 7EF8)
Macromolecule: Adenine DNA glycosylase
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 3.2.2.31
Sequence length: 458 residues
Sequence: GPGYQSLDGLAKQKREELLQASVSPYHLFSDVADVTAFRSNLLSWYDQEKRDLPWRNLAKEEANSDRRAYAVWVSEVMLQQTQVATVIDYYTRWMQKWPKLQDLASASLEEVNQLWSGLGYYSRGRRLQEGARKVVEELGGHMPRTAETLQQLLPGVGRYTAGAIASIAFDQVTGVVDGNVLRVLCRVRAIGADPTSTLVSHHLWNLAQQLVDPARPGDFNQAAMELGATVCTPQRPLCSHCPVQSLCRAYQRVQRGQLSALPGRPDIEECALNTRQCQLCLTSSSPWDPSMGVANFPRKASRRPPREEYSATCVVEQPGAIGGPLVLLVQRPDSGLLAGLWEFPSVTLEPSEQHQHKALLQELQRWCGPLPAIRLQHLGEVIHIFSHIKLTYQVYSLALDQAPASTAPPGARWLTWEEFCNAAVSTAMKKVFRMYEDHRQGTRKGSKRSQVCPPSSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.1976
R free: 0.2206
Average B factor: 75.38
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG3350, lithium sulfate, ammonium sulfate, Bis-Tris
Matthews coefficient: 2.61
Solvent content (%): 52.8
Ligand: IRON/SULFUR CLUSTER (SF4)
Ligand formula: Fe4 S4
Ligand molecular weight: 351.64
Ligand SMILES: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
Ligand InChI: InChI=1S/4Fe.4S
Release date: 2021-06-23
Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-A71 (fusion protein) (PDB entry 6HLW)
Macromolecule: Golgi resident protein GCP60
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 168 residues
Sequence: GAMESLPVIAAPSMWTRPQIKDFKEKIQQDADSVITVGRGEVVTVRVPTHEEGSYLFWEFATDNYDIGFGVYFEWTDSPNTAVSVHVSESSDDDEEEEENIGCEEKAKKNANKPLLDEIVPVYRRDCHEEVYAGSHQYPGRGVYLLKFDNSYSLWRSKSVYYRVYYTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.728
R work: 0.2422
R free: 0.2559
Average B factor: 75.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 5% w/v PEG 20.000, 25% v/v 1,1,1-tris(hydroxymethyl)propane, 1% w/v NDSB 201, 0.5 mM MgCl2, 0.5mM CoCl2, 0.5 mM NiCl2, 0.5 mM ZnCl2, 100 mM BES/TEA pH 7.5
Matthews coefficient: 2.7
Solvent content (%): 54.43
Release date: 2019-07-24
Crystal Structure human formylglycine generating enzyme E130D mutant (PDB entry 5SSX)
Macromolecule: Formylglycine-generating enzyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.8.3.7
Sequence length: 323 residues
Sequence: ADLGSSMEFEANAPGPVPGERQLAHSKMVPIPAGVFTMGTDDPQIKQDGEAPARRVTIDAFYMDAYDVSNTEFEKFVNSTGYLTEAEKFGDSFVFEGMLSEQVKTNIQQAVAAAPWWLPVKGANWRHPEGPDSTILHRPDHPVLHVSWNDAVAYCTWAGKRLPTEAEWEYSCRGGLHNRLFPWGNKLQPKGQHYANIWQGEFPVTNTGEDGFQGTAPVDAFPPNGYGLYNIVGNAWEWTSDWWTVHHSVEETLNPKGPPSGKDRVKKGGSYMCHRSYCYRYRCAARSQNTPDSSASNLGFRCAADRLPTMDSGRGSHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.02
R work: 0.123
R free: 0.1375
Average B factor: 14.0685
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 9.6 mg/mL protein in 20mM Tris/HCl pH8.0 mixed 1:1 with reservoir 0.1M Tris/HCl pH 8.5, 20-25% PEG4000, 0.2-0.3M CaCl2
Matthews coefficient: 2.03
Solvent content (%): 39.52
Ligand: COPPER (I) ION (CU1)
Ligand formula: Cu
Ligand molecular weight: 63.546
Ligand SMILES: [Cu+]
Ligand InChI: InChI=1S/Cu/q+1
Release date: 2023-08-23
Stable-5-LOX elongated Ha2 (4 copies ASU) (PDB entry 7TTL)
Macromolecule: Arachidonate 5-lipoxygenase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.34
Sequence length: 691 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMPSYTVTVATGSQEHAGTDDYIYLSLVGSAGCSEKHLLDKGSFERGAVDSYDVTVDEELGEIQLVRIEKRKYGSNDDWYLKYITLKTPHGDYIEFPCYRWITGDVEVVLRDGRAKLARDDQIHILKQHRRKELETRQKQYRWMEWNPGFPLSIDAKCHKDLPRDIQFDSEKGVDFVLNYSKAMENLFINRFMHMFQSSWNDFADFEKIFVKISNTISERVMNHWQEDLMFGYQFLNGANPVLIRRCTELPEKLPVTTEMVECSLERQLSLEQEVQQGNIFIVDFELLDGIDANKTDPCTLQFLAAPICLLYKNLANKIVPIAIQLNQIPGDENPIFLPSDAKYDWLLAKIWVRSSDFHVHQTITHLLRTHLVSEVFGIAMYRQLPAVHPIFKLLVAHVRFTIAINTKAREQLICECGLFDKANATGGGGHVQMVQRAMKDLTYASLCFPEAIKARGMESKEDIPYYFYRDDGLLVWEAIRTFTAEVVDIYYEGDQVVEEDPELQDFVNDVYVYGMRGRKSSGFPKSVKSREQLSEYLTVVIFTASAQHAAVNFGQYDWASWIPNAPPTMRAPPPTAKGVVTIEQIVDTLPDRGRSCWHLGAVWALSQFQENELFLGMYPEEHFIEKPVKEAMARFRKNLEAIVSVIAERNENLQLPYYYLSPDRIPNSVAI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.2147
R free: 0.2748
Average B factor: 65.339
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 10% Tacsimate
Matthews coefficient: 2.49
Solvent content (%): 50.7
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2022-08-31
Crystal Structure of human phosphodiesterase 10 in complex with 3-(2-chlorophenyl)-12-methoxy-5-methyl-2,4,8,13-tetrazatricyclo[7.4.0.02,6]trideca-1(9),3,5,7,10,12-hexaen-7-amine (PDB entry 5SHG)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.185
R free: 0.2255
Average B factor: 43.357
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.62
Solvent content (%): 53.03
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2022-10-12