Structure of PDB 2v3v Chain A Binding Site BS03

Receptor Information
>2v3v Chain A (length=721) Species: 876 (Desulfovibrio desulfuricans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRPEKWVKGVCRYCGTGCGVLVGVKDGKAVAIQGDPNNHNAGLLCLKGSL
LIPVLNSKERVTQPLVRRHKGGKLEPVSWDEALDLMASRFRSSIDMYGPN
SVAWYGSGQCLTEESYVANKIFKGGFGTNNVDGNPRLCMASAVGGYVTSF
GKDEPMGTYADIDQATCFFIIGSNTSEAHPVLFRRIARRKQVEPGVKIIV
ADPRRTNTSRIADMHVAFRPGTDLAFMHSMAWVIINEELDNPRFWQRYVN
FMDAEGKPSDFEGYKAFLENYRPEKVAEICRVPVEQIYGAARAFAESAAT
MSLWCMGINQRVQGVFANNLIHNLHLITGQICRPGATSFSLTGQPNACGG
VRDGGALSHLLPAGRAIPNAKHRAEMEKLWGLPEGRIAPEPGYHTVALFE
ALGRGDVKCMIICETNPAHTLPNLNKVHKAMSHPESFIVCIEAFPDAVTL
EYADLVLPPAFWCERDGVYGCGERRYSLTEKAVDPPGQCRPTVNTLVEFA
RRAGVDPQLVNFRNAEDVWNEWRMVSKGTTYDFWGMTRERLRKESGLIWP
CPSEDHPGTSLRYVRGQDPCVPADHPDRFFFYGKPDGRAVIWMRPAKGAA
EEPDAEYPLYLTSMRVIDHWHTATMTGKVPELQKANPIAFVEINEEDAAR
TGIKHGDSVIVETRRDAMELPARVSDVCRPGLIAVPFFDPKKLVNKLFLD
ATDPVSREPEYKICAARVRKA
Ligand information
Ligand IDMGD
InChIInChI=1S/C20H26N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1
InChIKeyVQAGYJCYOLHZDH-ILXWUORBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C1C=2NC3C(S)=C(S)C(OC3NC=2N=C(N)N1)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O
CACTVS 3.341NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
FormulaC20 H26 N10 O13 P2 S2
Name2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE;
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000195757106
PDB chain2v3v Chain A Residue 812 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2v3v Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes the Sixth Coordination of the Catalytic Molybdenum.
Resolution1.99 Å
Binding residue
(original residue number in PDB)
K49 G174 S175 A180 D204 P205 R206 F220 P222 D225 C307 M308 G309 G345 Q346 M616 R617 I619 H621 W622 H623 K714
Binding residue
(residue number reindexed from 1)
K47 G172 S173 A178 D202 P203 R204 F218 P220 D223 C305 M306 G307 G343 Q344 M614 R615 I617 H619 W620 H621 K712
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K49 S109 C140 M141 A180 M308 T344 G345 Q346
Catalytic site (residue number reindexed from 1) K47 S107 C138 M139 A178 M306 T342 G343 Q344
Enzyme Commision number 1.9.6.1: nitrate reductase (cytochrome).
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0008940 nitrate reductase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0030151 molybdenum ion binding
GO:0043546 molybdopterin cofactor binding
GO:0046872 metal ion binding
GO:0050140 nitrate reductase (cytochrome) activity
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006777 Mo-molybdopterin cofactor biosynthetic process
GO:0042128 nitrate assimilation
Cellular Component
GO:0042597 periplasmic space

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:2v3v, PDBe:2v3v, PDBj:2v3v
PDBsum2v3v
PubMed18327621
UniProtP81186|NAPA_DESDA Periplasmic nitrate reductase (Gene Name=napA)

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