Structure of PDB 2w54 Chain B Binding Site BS01

Receptor Information
>2w54 Chain B (length=760) Species: 1061 (Rhodobacter capsulatus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVGKPLPHDSARAHVTGQARYLDDLPCPANTLHLAFGLSTEASAAITGLD
LEPVRESPGVIAVFTAADLPHDNDASPAPSPEPVLATGEVHFVGQPIFLV
AATSHRAARIAARKARITYAPRPAILTLDQALAADSRFEGGPVIWARGDV
ETALAGAAHLAEGCFEIGGQEHFYLEGQAALALPAEGGVVIHCSSQHPSE
IQHKVAHALGLAFHDVRVEMRRMGGGFGGKESQGNHLAIACAVAARATGR
PCKMRYDRDDDMVITGKRHDFRIRYRIGADASGKLLGADFVHLARCGWSA
DLSLPVCDRAMLHADGSYFVPALRIESHRLRTNTQSNTAFRGFGGPQGAL
GMERAIEHLARGMGRDPAELRALNFYDPPEKKTQTTHYGQEVADCVLGEL
VTRLQKSANFTTRRAEIAAWNSTNRTLARGIALSPVKFGISFTLTHLNQA
GALVQIYTDGSVALNHGGTEMGQGLHAKMVQVAAAVLGIDPVQVRITATD
TSKVPNTSATAASSGADMNGMAVKDACETLRGRLAGFVAAREGCAARDVI
FDAGQVQASGKSWRFAEIVAAAYMARISLSATGFYATPKLSWDRLRGQGR
PFLYFAYGAAITEVVIDRLTGENRILRTDILHDAGASLNPALDIGQIEGA
YVQGAGWLTTEELVWDHCGRLMTHAPSTYKIPAFSDRPRIFNVALWDQPN
REETIFRSKAVGEPPFLLGISAFLALHDACAACGPHWPDLQAPATPEAVL
AAVRRAEGRA
Ligand information
Ligand IDXAX
InChIInChI=1S/C10H14N5O6PS2.Mo.H2O.O.S/c11-10-14-7-4(8(16)15-10)12-3-6(24)5(23)2(21-9(3)13-7)1-20-22(17,18)19;;;;/h2-3,9,12,23-24H,1H2,(H2,17,18,19)(H4,11,13,14,15,16);;1H2;;/q;+3;;;/p-3/t2-,3+,9-;;;;/m1..../s1
InChIKeyOIQYCPXIZLGKQT-BKZHXLINSA-K
SMILES
SoftwareSMILES
CACTVS 3.370NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P](O)(O)=O)C4=C3S[Mo](O)(=O)(=S)S4)C(=O)N1
OpenEye OEToolkits 1.7.2C(C1C2=C(C3C(O1)NC4=C(N3)C(=O)NC(=N4)N)S[Mo](=O)(=S)(S2)O)OP(=O)(O)O
OpenEye OEToolkits 1.7.2C([C@@H]1C2=C([C@H]3[C@@H](O1)NC4=C(N3)C(=O)NC(=N4)N)S[Mo](=O)(=S)(S2)O)OP(=O)(O)O
CACTVS 3.370NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(O)=O)C4=C3S[Mo](O)(=O)(=S)S4)C(=O)N1
ACDLabs 12.01O=P(O)(O)OCC2OC3NC=4N=C(NC(=O)C=4NC3C=1S[Mo](=O)(=S)(O)SC=12)N
FormulaC10 H13 Mo N5 O8 P S3
Name{[(5aR,8R,9aR)-2-amino-4-oxo-6,7-di(sulfanyl-kappaS)-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(hydroxy)oxo(thioxo)molybdenum
ChEMBL
DrugBank
ZINC
PDB chain2w54 Chain B Residue 1778 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2w54 Mechanism of Substrate and Inhibitor Binding of Rhodobacter Capsulatus Xanthine Dehydrogenase.
Resolution3.3 Å
Binding residue
(original residue number in PDB)
G227 F228 G229 F341 R342 M488 G489 Q490 A528 S530 G532 Q663 E730
Binding residue
(residue number reindexed from 1)
G226 F227 G228 F340 R341 M471 G472 Q473 A511 S513 G515 Q646 E713
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q197 E232 R310 H314 R342 G729 E730
Catalytic site (residue number reindexed from 1) Q196 E231 R309 H313 R341 G712 E713
Enzyme Commision number 1.1.1.204: Transferred entry: 1.17.1.4.
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0016491 oxidoreductase activity
GO:0030151 molybdenum ion binding
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:2w54, PDBe:2w54, PDBj:2w54
PDBsum2w54
PubMed19109249
UniProtO54051

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