satarupa22/MacromolecularLigandDB huggingface dataset:
JmjC domain-containing protein 5 (JMJD5) in complex with Mn and (S)-2-(1-hydroxy-2,5-dioxopyrrolidin-3-yl)acetic acid (PDB entry 7UQ3)
Macromolecule: Bifunctional peptidase and arginyl-hydroxylase JMJD5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.73
Sequence length: 256 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.1339
R free: 0.1349
Average B factor: 21.1625
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: Sample: 22 mg/mL JMJD5, 1.5 mM MnCl2, 5 mM compound (IS-52); Reservoir: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2; Cryo-protection: 25% (v/v) glycerol; Method: 300 nL sitting drops (sample:well, 2:1 ratio)
Matthews coefficient: 2.11
Solvent content (%): 41.58
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2022-12-21
DNA Polymerase Mu, 8-oxorGTP:Ct Ternary Complex, 50 mM Mg2+ (2160 min) (PDB entry 6VF9)
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: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.165
R free: 0.1818
Average B factor: 26.8957
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: 2.45
Solvent content (%): 49.89
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: 2021-09-01
Structure of cyclophilin A in complex with 3-methylpyridin-2-amine (PDB entry 5NOR)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.15997
R free: 0.20344
Average B factor: 16.579
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.75
Solvent content (%): 55.32
Ligand: 3-methylpyridin-2-amine (93Q)
Ligand formula: C6 H8 N2
Ligand molecular weight: 108.141
Ligand SMILES: Cc1cccnc1N
Ligand InChI: InChI=1S/C6H8N2/c1-5-3-2-4-8-6(5)7/h2-4H,1H3,(H2,7,8)
Release date: 2017-07-12
Structure of Human Cytochrome P450 1A1 with Duocarmycin Prodrug (S) ICT-2700 (PDB entry 6UDL)
Macromolecule: Cytochrome P450 1A1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.1
Sequence length: 491 residues
Sequence: MAKKTSSKGLKNPPGPWGWPLIGHMLTLGKNPHLALSRMSQQYGDVLQIRIGSTPVVVLSGLDTIRQALVRQGDDFKGRPDLYTFTLISNGQSMSFSPDSGPVWAARRRLAQNGLKSFSIASDPASSTSCYLEEHVSKEAEVLISTLQELMAGPGHFNPYRYVVVSVTNVICAICFGRRYDHNHQELLSLVNLNNNFGEVVGSGNPADFIPILRYLPNPSLNAFKDLNEKFYSFMQKMVKEHYKTFEKGHIRDITDSLIEHCQEKQLDENANVQLSDEKIINIVLDLFGAGFDTVTTAISWSLMYLVMNPRVQRKIQEELDTVIGRSRRPRLSDRSHLPYMEAFILETFRHSSFVPFTIPHSTTRDTSLKGFYIPKGRCVFVNQWQINHDQKLWVNPSEFLPERFLTPDGAIDKVLSEKVIIFGMGKRKCIGETIARWEVFLFLAILLQRVEFSVPLGVKVDMTPIYGLTMKHACCEHFQMQLRSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2378
R free: 0.2867
Average B factor: 75.1579
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.18 M sodium phosphate dibasic, 18% PEG3350, 5 mM (S)-O-methyl-serine dodecylamide hydrochloride
Matthews coefficient: 3.52
Solvent content (%): 65.09
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2020-09-23
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOMB000144a (PDB entry 5QF4)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.832
R work: 0.1935
R free: 0.2263
Average B factor: 45.3889
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.35
Solvent content (%): 63.23
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2018-10-10
Discovery of IRAK4 Inhibitor 38 (PDB entry 8ATN)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 298 residues
Sequence: GSFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIAAAIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.171
R work: 0.2384
R free: 0.3059
Average B factor: 77.038
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.9
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium acetate buffer pH 4.9, 1.5-1.7M ammonium citrate, 0.02M hexaaminecobalt(III)chloride
Matthews coefficient: 2.78
Solvent content (%): 55.92
Ligand: ~{N}-[3-methyl-2-(3-methyl-3-oxidanyl-butyl)-6-(2-oxidanylpropan-2-yl)benzimidazol-5-yl]-6-(trifluoromethyl)pyridine-2-carboxamide (O06)
Ligand formula: C23 H27 F3 N4 O3
Ligand molecular weight: 464.481
Ligand SMILES: CC(C)(CCc1nc2cc(c(cc2n1C)NC(=O)c3cccc(n3)C(F)(F)F)C(C)(C)O)O
Ligand InChI: InChI=1S/C23H27F3N4O3/c1-21(2,32)10-9-19-28-16-11-13(22(3,4)33)15(12-17(16)30(19)5)29-20(31)14-7-6-8-18(27-14)23(24,25)26/h6-8,11-12,32-33H,9-10H2,1-5H3,(H,29,31)
Release date: 2023-09-06
Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain bound with N46 (PDB entry 6C0T)
Macromolecule: cGMP-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 347 residues
Sequence: GSGLDDVSNKAYEDAEAKAKYEAEAAFFANLKLSDFNIIDTLGVGGFGRVELVQLKSEESKTFAMKILKKRHIVDTRQQEHIRSEKQIMQGAHSDFIVRLYRTFKDSKYLYMLMEACLGGELWTILRDRGSFEDSTTRFYTACVVEAFAYLHSKGIIYRDLKPENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGILMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPKKIAKNAANLIKKLCRDNPSERLGNLKNGVKDIQKHKWFEGFNWEGLRKGTLTPPIIPSVASPTDTSNFDSFPEDNDEPPPDDNSGWDIDF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.2072
R free: 0.2438
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 24%w/v PEG1500, 20%v/v glycerol, 3% w/v Trimethylamine N-oxide dihydrate
Matthews coefficient: 2.36
Solvent content (%): 47.84
Ligand: N-[(3R,4R)-4-{[4-(2-fluoro-3-methoxy-6-propoxybenzene-1-carbonyl)benzene-1-carbonyl]amino}pyrrolidin-3-yl]-1H-indazole-5-carboxamide (EE4)
Ligand formula: C30 H30 F N5 O5
Ligand molecular weight: 559.588
Ligand SMILES: CCCOc1ccc(c(c1C(=O)c2ccc(cc2)C(=O)NC3CNCC3NC(=O)c4ccc5c(c4)cn[nH]5)F)OC
Ligand InChI: InChI=1S/C30H30FN5O5/c1-3-12-41-24-10-11-25(40-2)27(31)26(24)28(37)17-4-6-18(7-5-17)29(38)34-22-15-32-16-23(22)35-30(39)19-8-9-21-20(13-19)14-33-36-21/h4-11,13-14,22-23,32H,3,12,15-16H2,1-2H3,(H,33,36)(H,34,38)(H,35,39)/t22-,23-/m1/s1
Release date: 2018-05-30
Crystal structure of human Cathepsin-S with bound ligand (PDB entry 5QCB)
Macromolecule: Cathepsin S
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.27
Sequence length: 223 residues
Sequence: ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEILQGGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.194
R free: 0.256
Average B factor: 13.25
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 2.25
Solvent content (%): 45.33
Ligand: tert-butyl 4-(2-{3-[3-{[(3-methylbut-2-enoyl)amino]methyl}-4-(trifluoromethyl)phenyl]-1-[3-(morpholin-4-yl)propyl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl}-2-oxoethyl)piperidine-1-carboxylate (BHV)
Ligand formula: C38 H53 F3 N6 O5
Ligand molecular weight: 730.86
Ligand SMILES: CC(=CC(=O)NCc1cc(ccc1C(F)(F)F)c2c3c(n(n2)CCCN4CCOCC4)CCN(C3)C(=O)CC5CCN(CC5)C(=O)OC(C)(C)C)C
Ligand InChI: InChI=1S/C38H53F3N6O5/c1-26(2)21-33(48)42-24-29-23-28(7-8-31(29)38(39,40)41)35-30-25-46(16-11-32(30)47(43-35)13-6-12-44-17-19-51-20-18-44)34(49)22-27-9-14-45(15-10-27)36(50)52-37(3,4)5/h7-8,21,23,27H,6,9-20,22,24-25H2,1-5H3,(H,42,48)
Release date: 2017-12-20
Structure of human Phospholipase D2 catalytic domain (PDB entry 6OHO)
Macromolecule: Phospholipase D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.4
Sequence length: 640 residues
Sequence: SSYRQARWWAQEITELAQGPGRDFLQLHRHDSYAPPRPGTLARWFVNGAGYFAAVADAILRAQEEIFITDWWLSPEVYLKRPAHSDDWRLDIMLKRKAEEGVRVSILLFKEVELALGINSGYSKRALMLLHPNIKVMRHPDQVTLWAHHEKLLVVDQVVAFLGGLDLAYGRWDDLHYRLTDLGDSSESAASQPPTPRPDSPATPDLSHNQFFWLGKDYSNLITKDWVQLDRPFEDFIDRETTPRMPWRDVGVVVHGLPARDLARHFIQRWNFTKTTKAKYKTPTYPYLLPKSTSTANQLPFTLPGGQCTTVQVLRSVDRWSAGTLENSILNAYLHTIRESQHFLYIENQFFISCSDGRTVLNKVGDEIVDRILKAHKQGWCYRVYVLLPLLPGFEGDISTGGGNSIQAILHFTYRTLCRGEYSILHRLKAAMGTAWRDYISICGLRTHGELGGHPVSELIYIHSKVLIADDRTVIIGSANINDRSLLGKRDSELAVLIEDTETEPSLMNGAEYQAGRFALSLRKHCFGVILGANTRPDLDLRDPICDDFFQLWQDMAESNANIYEQIFRCLPSNATRSLRTLREYVAVEPLATVSPPLARSELTQVQGHLVHFPLKFLEDESLLPPLGSKEGMIPLEVWT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1813
R free: 0.2239
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 298
Crystal growth procedure: 0.2M ammonium sulfate, 20% PEG3350, 0.1M bis-tris pH 6.7
Matthews coefficient: 2.06
Solvent content (%): 40.27
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: 2020-02-19
Crystal structure of human KDM4A in complex with compound 17e (PDB entry 6H4Y)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 360 residues
Sequence: SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.174
R free: 0.209
Average B factor: 70.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Matthews coefficient: 2.47
Solvent content (%): 50.13
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: 2019-06-12
Structure of Human Neurolysin in complex with dynorphin A8(1-8) peptide (PDB entry 8VJV)
Macromolecule: Neurolysin, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.16
Sequence length: 667 residues
Sequence: SSYTVAGRNVLRWDLSPEQIKTRTEELIVQTKQVYDAVGMLGIEEVTYENCLQALADVEVKYIVERTMLDFPQHVSSDKEVRAASTEADKRLSRFDIEMSMRGDIFERIVHLQETCDLGKIKPEARRYLEKSIKMGKRNGLHLPEQVQNEIKSMKKRMSELCIDFNKNLNEDDTFLVFSKAELGALPDDFIDSLEKTDDDKYKITLKYPHYFPVMKKCCIPETRRRMEMAFNTRCKEENTIILQQLLPLRTKVAKLLGYSTHADFVLEMNTAKSTSRVTAFLDDLSQKLKPLGEAEREFILNLKKKECKDRGFEYDGKINAWDLYYYMTQTEELKYSIDQEFLKEYFPIEVVTEGLLNTYQELLGLSFEQMTDAHVWNKSVTLYTVKDKATGEVLGQFYLDLYPREGKYNHAACFGLQPGCLLPDGSRMMAVAALVVNFSQPVAGRPSLLRHDEVRTYFHEFGHVMHQICAQTDFARFSGTNVETDFVEVPSQMLENWVWDVDSLRRLSKHYKDGSPIADDLLEKLVASRLVNTGLLTLRQIVLSKVDQSLHTNTSLDAASEYAKYCSEILGVAATPGTNMPATFGHLAGGYDGQYYGYLWSEVFSMDMFYSCFKKEGIMNPEVGMKYRNLILKPGGSLDGMDMLHNFLKREPNQKAFLMSRGLHAP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.2131
R free: 0.2492
Average B factor: 49.11
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Matthews coefficient: 2.62
Solvent content (%): 53.08
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: 2024-08-21
Crystal structure of the human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion (maltose bound form) in complex with the designed AR protein mbp3_16 (PDB entry 6D67)
Macromolecule: Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Escherichia coli K-12
EC number: 3.1.3.16
Sequence length: 520 residues
Sequence: MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAGGPVEILPFLYLGSAYHASRKDMLDALGITALINVSANCPNHFEGHYQYKSIPVEDNHKADISSWFNEAIDFIDSIKNAGGRVFVHSQAGISRSATICLAYLMRTNRVKLDEAFEFVKQRRSIISPNFSFMGQLLQFESQVLAHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.1819
R free: 0.2517
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M DL-GLUTAMIC ACID
0.2 M DL-ALANINE
0.2 M GLYCINE
0.2 M DL-LYSINE
0.2 M DL-SERINE
0.1 M TRIS; BICINE
25% MPD
25% PEG1000
25% PEG3350
Matthews coefficient: 2.35
Solvent content (%): 47.65
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2018-09-19
Crystal Structure of ERK2 in complex with 7-(1-propyl-1H-pyrazol-4-yl)-2-(pyridin-4-yl)-5H-pyrrolo[2,3-b]pyrazine (PDB entry 4QP9)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 369 residues
Sequence: MGSHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.001
R work: 0.1843
R free: 0.227
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG3350, 0.2 M proline, and 0.1 M HEPES pH7.5, in a 24-well Linbro plates incubated at 4C, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2
Solvent content (%): 38.61
Ligand: 7-(1-propyl-1H-pyrazol-4-yl)-2-(pyridin-4-yl)-5H-pyrrolo[2,3-b]pyrazine (35X)
Ligand formula: C17 H16 N6
Ligand molecular weight: 304.349
Ligand SMILES: CCCn1cc(cn1)c2c[nH]c3c2nc(cn3)c4ccncc4
Ligand InChI: InChI=1S/C17H16N6/c1-2-7-23-11-13(8-21-23)14-9-19-17-16(14)22-15(10-20-17)12-3-5-18-6-4-12/h3-6,8-11H,2,7H2,1H3,(H,19,20)
Release date: 2015-09-23
Crystal Structure of apo human cyclic GMP-AMP synthase (PDB entry 7FTJ)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.461
R work: 0.1905
R free: 0.2101
Average B factor: 32.5084
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals.
Matthews coefficient: 1.98
Solvent content (%): 37.72
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: 2024-02-21
Crystal structure of human exonuclease 1 Exo1 (D225A) in complex with 5' recessed-end DNA (rVIII) (PDB entry 5V0A)
Macromolecule: Exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 358 residues
Sequence: MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCAYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSRENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.211
R free: 0.247
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 290
Crystal growth procedure: 100 mM sodium acetate, pH 7.0, 10 mM potassium chloride, 2-4% PEG4000
Matthews coefficient: 2.43
Solvent content (%): 49.29
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2017-05-24
Crystallographic structure of the catalytic domain of Human Phenylalanine Hydroxylase (hPAH CD) in complex with iron at 1.6 Angstrom (PDB entry 6HPO)
Macromolecule: Phenylalanine-4-hydroxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.16.1
Sequence length: 452 residues
Sequence: MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDVNLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYMEEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGFRLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFAQFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSEKPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQRIEVLDNTQQLKILADSINSEIGILCSALQKIK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.1607
R free: 0.177
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291
Crystal growth procedure: 40 mM PIPES, 20% PEG 2000, pH 6.8
Matthews coefficient: 2.48
Solvent content (%): 50.35
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2019-06-05
X-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-yl)pyridine (PDB entry 7JU8)
Macromolecule: Collagenase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24
Sequence length: 171 residues
Sequence: YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1978
R free: 0.2642
Average B factor: 21.911
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 10% w/v PEG4000, 1 M ammonium formate, and 100 mM Tris, pH 8.0
Matthews coefficient: 2.31
Solvent content (%): 46.77
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: 2021-08-04