Structure of PDB 3ml1 Chain A Binding Site BS02

Receptor Information
>3ml1 Chain A (length=799) Species: 381666 (Cupriavidus necator H16) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTDSEVTKLKWSKAPCRFCGTGCGVTVAVKDNKVVATQGDPQAEVNKGLN
CVKGYFLSKIMYGQDRLTRPLMRMKNGKYDKNGDFAPVTWDQAFDEMERQ
FKRVLKEKGPTAVGMFGSGQWTVWEGYAAAKLYKAGFRSNNIDPNARHCM
ASAAAGFMRTFGMDEPMGCYDDFEAADAFVLWGSNMAEMHPILWTRVTDR
RLSHPKTRVVVLSTFTHRCFDLADIGIIFKPQTDLAMLNYIANYIIRNNK
VNKDFVNKHTVFKEGVTDIGYGLRPDHPLQKAAKNASDPGAAKVITFDEF
AKFVSKYDADYVSKLSAVPKAKLDQLAELYADPNIKVMSLWTMGFNQHTR
GTWANNMVYNLHLLTGKIATPGNSPFSLTGQPSACGTAREVGTFSHRLPA
DMVVTNPKHREEAERIWKLPPGTIPDKPGYDAVLQNRMLKDGKLNAYWVQ
VNNNMQAAANLMEEGLPGYRNPANFIVVSDAYPTVTALAADLVLPSAMWV
EKEGAYGNAERRTQFWHQLVDAPGEARSDLWQLVEFAKRFKVEEVWPPEL
IAKKPEYKGKTLYDVLYRNGQVDKFPLKDVNAEYHNAEAKAFGFYLQKGL
FEEYATFGRGHGHDLAPFDAYHEARGLRWPVVNGKETRWRYREGSDPYVK
AGTGFQFYGNPDGKAVIFALPYEPPAESPDKEYPYWLVTGRVLEHWHSGS
MTRRVPELYRSFPNAVVFMHPEDAKALGLRRGVEVEVVSRRGRMRSRIET
RGRDAPPRGLVFVPWFDASQLINKVTLDATCPISLQTDFKKCAVKIVKV
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 chain3ml1 Chain A Residue 1803 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ml1 The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states
Resolution1.6 Å
Binding residue
(original residue number in PDB)
R20 Q123 N148 H151 C152 Q350 Q384 V454 N455 N456 A460 S482 D483 S499 M501 K505 D532 T692 R694 W699 H700 S701 S703 W768 N776 F792
Binding residue
(residue number reindexed from 1)
R17 Q120 N145 H148 C149 Q347 Q381 V451 N452 N453 A457 S479 D480 S496 M498 K502 D529 T689 R691 W696 H697 S698 S700 W765 N773 F789
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) N53 C54 K56 G122 W124 C152 M153 M346 T382 G383 Q384
Catalytic site (residue number reindexed from 1) N50 C51 K53 G119 W121 C149 M150 M343 T379 G380 Q381
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
GO:0045333 cellular respiration
Cellular Component
GO:0042597 periplasmic space
GO:1990204 oxidoreductase complex

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:3ml1, PDBe:3ml1, PDBj:3ml1
PDBsum3ml1
PubMed21419779
UniProtP39185|NAPA_CUPNH Periplasmic nitrate reductase (Gene Name=napA)

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