Structure of PDB 3ml1 Chain A Binding Site BS01

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 IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain3ml1 Chain A Residue 1801 [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)		C19 C22 T24 C26 N53 C54
Binding residue
(residue number reindexed from 1)		C16 C19 T21 C23 N50 C51
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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