satarupa22/MacromolecularLigandDB huggingface dataset:
GTB mutant with mercury - E303A (PDB entry 5CQL)
Macromolecule: Histo-blood group ABO system transferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.40
Sequence length: 294 residues
Sequence: FMVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVGAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPSFYGSSREAFTYERRPQSQAYIPKDEGDFYYMGAFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDASHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPKNHQAVRNPE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1744
R free: 0.2065
Average B factor: 31.987
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 10 ul drops with 6-8 mg/ml protein, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA) pH 7.5, 50 mM, sodium acetate pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 5%(v/v) glycerol, 2%(w/v) PEG 4000, and 0.3-0.5 mM 3-chloromercuri-2-methoxypropylurea suspended over 1 ml of a resevoir solution: 50 mM ADA pH 7.5, 10 mM MnCl2, 100 mM ammonium sulfate, 5%(v/v) MPD, 10%(v/v) glycerol, and 8-10%(w/v) PEG 4000
Matthews coefficient: 2.28
Solvent content (%): 46.09
Ligand: MERCURY (II) ION (HG)
Ligand formula: Hg
Ligand molecular weight: 200.59
Ligand SMILES: [Hg+2]
Ligand InChI: InChI=1S/Hg/q+2
Release date: 2016-10-26
STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND O) (PDB entry 6XEC)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 376 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.701
R work: 0.1752
R free: 0.2032
Average B factor: 30.25
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
Matthews coefficient: 2.48
Solvent content (%): 50.47
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: 2020-08-12
Crystal structure of Tie2-agonistic antibody in complex with human Tie2 Fn2-3 (PDB entry 7E72)
Macromolecule: the chimeric Fab fragment of 3H7 (heavy chain)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 227 residues
Sequence: QVQLQQPGAELVRPGASVKLSCKASGYSFTSYWMNWVKQRPGQGLEWIGMIHPSDSETRLNQKFMDKATLTVDKSSSTAYMQLSSPTSEDSAVYYCARGLYGNSWGQGTLVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.094
R work: 0.1826
R free: 0.2331
Average B factor: 39.2863
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292.15
Crystal growth procedure: 100 mM Bis-Tris propane pH 8.5, 110 mM potassium dihydrogen phosphate, 15% (w/v) polyethylene glycol 3350
Matthews coefficient: 2.92
Solvent content (%): 57.82
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: 2021-11-10
Crystal structure of the bromodomain of human CREBBP in complex with UP39 (PDB entry 5ENG)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1641
R free: 0.1725
Average B factor: 15.1463
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M KSCN, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Matthews coefficient: 2.4
Solvent content (%): 48.82
Ligand: methyl 2-[2-(3,5-dihydro-2~{H}-pyrazin-4-yl)ethoxy]-5-[(5-ethanoyl-2-ethoxy-phenyl)carbamoyl]benzoate (5QN)
Ligand formula: C25 H29 N3 O6
Ligand molecular weight: 467.514
Ligand SMILES: CCOc1ccc(cc1NC(=O)c2ccc(c(c2)C(=O)OC)OCCN3CCN=CC3)C(=O)C
Ligand InChI: InChI=1S/C25H29N3O6/c1-4-33-23-8-5-18(17(2)29)16-21(23)27-24(30)19-6-7-22(20(15-19)25(31)32-3)34-14-13-28-11-9-26-10-12-28/h5-9,15-16H,4,10-14H2,1-3H3,(H,27,30)
Release date: 2016-11-23
Crystal structure of mammalian calcineurin (PDB entry 4ORC)
Macromolecule: Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 544 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMAAPEPARAAPPPPPPPPPPPGADRVVKAVPFPPTHRLTSEEVFDLDGIPRVDVLKNHLVKEGRVDEEIALRIINEGAAILRREKTMIEVEAPITVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWVLKILYPSTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYEACMEAFDSLPLAALLNQQFLCVHGGLSPEIHTLDDIRRLDRFKEPPAFGPMCDLLWSDPSEDFGNEKSQEHFSHNTVRGCSYFYNYPAVCEFLQNNNLLSIIRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLSICSDDELMTEGEDQFDGSAAARKEIIRNKIRAIGKMARVFSVLREESESVLTLKGLTPTGMLPSGVLAGGRQTLQSATVEAIEAEKAIRGFSPPHRICSFEEAKGLDRINERMPPRKDAVQQDGFNSLNTAHATENHGTGNHTAQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2153
R free: 0.2603
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.1
Crystallization temperature (K): 294
Crystal growth procedure: 100mM MES, pH 6.1, 10% PEG3350, 0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Matthews coefficient: 3.07
Solvent content (%): 59.96
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: 2015-05-20
Crystal Structure of Human Renin in Complex with a biphenylpipderidinylcarbinol (PDB entry 5VPM)
Macromolecule: Renin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.15
Sequence length: 337 residues
Sequence: GNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.20158
R free: 0.26045
Average B factor: 58.345
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 19-22% PEG3350, 0.2M ammonium sulfate, 0.1M TRIS-HCl, pH 7.5
Matthews coefficient: 2.83
Solvent content (%): 56.57
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: 2017-10-18
The Crystal Structure of EphA2 from Biortus. (PDB entry 8XPV)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 305 residues
Sequence: DPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1641
R free: 0.1903
Average B factor: 17.476
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Sodium Acetate, 0.1M Sodium Cacodylate HCl pH6.5, 18% PEG 8000
Matthews coefficient: 1.98
Solvent content (%): 37.98
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: 2024-01-24
Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20) (PDB entry 7KBG)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 376 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.26
R work: 0.1841
R free: 0.1964
Average B factor: 20.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5
Matthews coefficient: 2.46
Solvent content (%): 50.08
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2020-12-30
Human Fen1 in complex with an N-hydroxyurea compound (PDB entry 5FV7)
Macromolecule: FLAP ENDONUCLEASE 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 353 residues
Sequence: MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTLEVLFQGPGGGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.84
R work: 0.23387
R free: 0.30021
Average B factor: 24.792
Crystallization pH: 7.5
Crystal growth procedure: 25% PEG3350, 0.1M MOPS 7.0, 5% 2-PROPANOL, 2% GLYCEROL, pH 7.5
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: 2016-08-17
Structure of the M5 muscarinic acetylcholine receptor (M5-T4L) bound to tiotropium (PDB entry 6OL9)
Macromolecule: Muscarinic acetylcholine receptor M5, T4 Lysozyme fusion
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 480 residues
Sequence: GAPLERHRLWEVITIAAVTAVVSLITIVGNVLVMISFKVNSQLKTVNNYYLLSLACADLIIGIFSMNLYTTYILMGRWALGSLACDLWLALDYVASNARVMNLLVISFDRYFSITRPLTYRAKRTPKRAGIMIGLAWLISFILWAPAILCWQYLVGKRTVPLDECQIQFLSEPTITFGTAIAAFYIPVSVMTILYCRIYRETEKRTNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYRVVLVKERKAAQTLSAILLAFIITWTPYNIMVLVSTFCDKCVPVTLWHLGYWLCYVNSTVNPICYALCNRTFRKTFKMLLLCRWKKKKVEEKLYWQGNSKLPSSHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.541
R work: 0.2362
R free: 0.2573
Average B factor: 93.8622
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: Reconstituted in 10:1 monoolein:cholesterol mix, 100 mM D-L Malic acid pH 6.0, 220-280 mM ammonium tartrate dibasic, 37-41% PEG 400
Matthews coefficient: 2.5
Solvent content (%): 50.76
Ligand: OLEIC ACID (OLA)
Ligand formula: C18 H34 O2
Ligand molecular weight: 282.461
Ligand SMILES: CCCCCCCCC=CCCCCCCCC(=O)O
Ligand InChI: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9-
Release date: 2019-12-11
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z33545544 (PDB entry 5RYE)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2295
R free: 0.2696
Average B factor: 22.013
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.1
Solvent content (%): 41.43
Ligand: N~1~-phenylpiperidine-1,4-dicarboxamide (T0J)
Ligand formula: C13 H17 N3 O2
Ligand molecular weight: 247.293
Ligand SMILES: c1ccc(cc1)NC(=O)N2CCC(CC2)C(=O)N
Ligand InChI: InChI=1S/C13H17N3O2/c14-12(17)10-6-8-16(9-7-10)13(18)15-11-4-2-1-3-5-11/h1-5,10H,6-9H2,(H2,14,17)(H,15,18)
Release date: 2020-11-11
Structure of a proline specific mutant of human cathepsin L (PDB entry 6JD8)
Macromolecule: Cathepsin L1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.15
Sequence length: 360 residues
Sequence: MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKMTLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSSWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGYMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDLDHAVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASLASYPTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.457
R work: 0.1916
R free: 0.2369
Average B factor: 31.3457
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: PEG 4000, 2-propanol
Matthews coefficient: 1.8
Solvent content (%): 31.66
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: 2020-02-05
Crystal structure of a human calcineurin mutant (PDB entry 4ORA)
Macromolecule: Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 544 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMAAPEPARAAPPPPPPPPPPPGADRVVKAVPFPPTHRLTSEEVFDLDGIPRVDVLKNHLVKEGRVDEEIALRIINEGAAILRREKTMIEVEAPITVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWVLKILYPSTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYEACMEAFDSLPLAALLNQQFLCVHGGLSPEIHTLDDIRRLDRFKEPPAFGPMCDLLWSDPSEDFGNEKSQEHFSHNTVRGCSYFYNYPAVCEFLQNNNLLSIIRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLSICSDDELMTEGEDQFDGSAAARKEIIRNKIRAIGKMARYLSVLREESESVLTLKGLTPTGMLPSGVLAGGRQTLQSATVEAIEAEKAIRGFSPPHRICSFEEAKGLDRINERMPPRKDAVQQDGFNSLNTAHATENHGTGNHTAQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.747
R work: 0.1991
R free: 0.249
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 294
Crystal growth procedure: 100 mM MES, pH 5.8, 9% PEG 3350, 4% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Matthews coefficient: 2.98
Solvent content (%): 58.75
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: 2015-05-20
Crystal structure of human tyrosinase related protein 1 (PDB entry 5M8L)
Macromolecule: 5,6-dihydroxyindole-2-carboxylic acid oxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.18
Sequence length: 446 residues
Sequence: QFPRQCATVEALRSGMCCPDLSPVSGPGTDRCGSSSGRGRCEAVTADSRPHSPQYPHDGRDDREVWPLRFFNRTCHCNGNFSGHNCGTCRPGWRGAACDQRVLIVRRNLLDLSKEEKNHFVRALDMAKRTTHPLFVIATRRSEEILGPDGNTPQFENISIYNYFVWTHYYSVKKTFLGVGQESFGEVDFSHEGPAFLTWHRYHLLRLEKDMQEMLQEPSFSLPYWNFATGKNVCDICTDDLMGSRSNFDSTLISPNSVFSQWRVVCDSLEDYDTLGTLCNSTEDGPIRRNPAGNVARPMVQRLPEPQDVAQCLEVGLFDTPPFYSNSTNSFRNTVEGYSDPTGKYDPAVRSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFDEWLRRYNADISTFPLENAPIGHNRQYNMVPFWPPVTNTEMFVTAPDNLGYTYEIQWPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.214
R free: 0.2549
Average B factor: 39.7985
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: 0.1 M Tris (pH 7.0),
0.2 M NaCl and 30% (w/v) PEG 3000
Matthews coefficient: 3.03
Solvent content (%): 59.47
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: 2017-07-12
Crystal structure of Aurora-A kinase in complex with an allosterically binding fragment (PDB entry 5OSE)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1895
R free: 0.237
Average B factor: 53.6501
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350
Matthews coefficient: 2.76
Solvent content (%): 55.43
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2017-11-01
Crystal structure of GTB + B trisaccharide (native) (PDB entry 5TJN)
Macromolecule: Histo-blood group ABO system transferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.40
Sequence length: 297 residues
Sequence: AIGEFMVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVGAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPSFYGSSREAFTYERRPQSQAYIPKDEGDFYYMGAFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPKNHQAVRNP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.1832
R free: 0.2044
Average B factor: 21.136
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: Native crystals of GTA/GTB lacking any heavy metals were grown at 4 degrees Celsius from much higher concentrations of protein (30-40 mg/mL for GTB and 16-20 mg/mL for GTA) along with 1% PEG 4000, 4.5-5% 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA buffer pH 7.5, 30 mM sodium acetate buffer pH 4.6 and 5 mM MnCl2 for GTB crystallization and 5-8 mM CoCl2 for GTA crystallization.  10-15 microlitre drops were placed against a reservoir containing 3.7% PEG 4000, 7% MPD, 0.3 M ammonium sulfate, 0.25 M sodium chloride, 0.2 M ADA buffer and 0.1 M sodium acetate.  The crystals were usually grown for 5-10 days. Before making complexes, crystals of GTA/GTB were washed with modified mother liquor ML-2 consisting of 3.5% PEG 4000, 50 mM ammonium sulfate, 40 mM sodium chloride, 35 mM ADA buffer and 15% MPD or glycerol. Crystals of native GTA/GTB in complex with the respective A or B trisaccharide were obtained by soaking them in mother liquor ML-2 with 15% glycerol or MPD and 45-50 mM of each substrate for 2-5 days at 4 degrees Celsius.  Before freezing the crystals for data collection, the concentration of the cryoprotectant was made 30% glycerol or 20% MPD respectively
Matthews coefficient: 2.26
Solvent content (%): 45.55
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2017-06-14
Crystal structure of human butyrylcholinesterase in complex with (2-((1-(benzenesulfonyl)-1H-indol-4-yl)oxy)ethyl)(benzyl)amine (PDB entry 7AWG)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 529 residues
Sequence: EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1728
R free: 0.1974
Average B factor: 43.63
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate
Matthews coefficient: 3.2
Solvent content (%): 61.58
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: 2021-09-29
MUL1-RING domain (PDB entry 6M2D)
Macromolecule: Mitochondrial ubiquitin ligase activator of NFKB 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 57 residues
Sequence: GSLKSACVVCLSSFKSCVFLECGHVCSCTECYRALPEPKKCPICRQAITRVIPLYNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.795
R work: 0.1716
R free: 0.2272
Average B factor: 23.5384
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.4 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350
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: 2021-04-07