Structure of PDB 1ogy Chain K Binding Site BS05

Receptor Information
>1ogy Chain K (length=789) Species: 1063 (Cereibacter sphaeroides) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IRWSKAPCRFCGTGCGVMVGTRDGQVVATHGDTQAEVNRGLNCVKGYFLS
KIMYGEDRLTTPLLRMKDGVYHKEGEFAPVSWDEAFDVMAAQAKLVLKEK
APEAVGMFGSGQWTIWEGYAASKLMRAGFRSNNLDPNARHCMASAATAFM
RTFGMDEPMGCYDDFEAADAFVLWGSNMAEMHPILWSRLTDRRLSHEHVR
VAVLSTFTHRSSDLSDTPIIFRPGTDRAILNYIAHHIISTGRVNRDFVDR
HTNFALGATDIGYGLRPEHQLQLAAKGAADAGAMTPTDFETFAALVSEYT
LEKAAEISGVEPALLEELAELYADPDRKWMSLWTMGFNQHVRGVWANHMV
YNLHLLTGKISEPGNSPFSLTGQPFACGTAREVGTFAHRLPADMVVTNPE
HRAHAEEIWKLPAGLLPDWVGAHAVEQDRKLHDGEINFYWVQVNNNMQAA
PNIDQETYPGYRNPENFIVVSDAYPTVTGRAADLVLPAAMWVEKEGAYGN
AERRTHFWHQLVEAPGEARSDLWQLMEFSKRFTTDEVWPEEILSAAPAYR
GKTLFEVLFANGSVDRFPASDVNPDHANHEAALFGFYPQKGLFEEYAAFG
RGHGHDLAPFDTYHEVRGLHWPVVEGEETRWRYREGFDPYVKPGEGLRFY
GKPDGRAVILGVPYEPPAESPDEEFGFWLVTGRVLEHWHSGSMTLRWPEL
YKAFPGAVCFMHPEDARSRGLNRGSEVRVISRRGEIRTRLETRGRNRMPR
GVVFVPWFDASQLINKVTLDANDPISRQTDFKKCAVKIE
Ligand information
Ligand IDHEC
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
InChIKeyHXQIYSLZKNYNMH-LJNAALQVSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
OpenEye OEToolkits 1.5.0CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
CACTVS 3.341C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
CACTVS 3.341CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
FormulaC34 H34 Fe N4 O4
NameHEME C
ChEMBL
DrugBank
ZINC
PDB chain1ogy Chain L Residue 1129 [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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PDB1ogy Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase
Resolution3.2 Å
Binding residue
(original residue number in PDB)		L52 Y58
Binding residue
(residue number reindexed from 1)		L41 Y47
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) N42 C43 K45 G111 W113 C141 M142 M335 T371 G372 Q373
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:1ogy, PDBe:1ogy, PDBj:1ogy
PDBsum1ogy
PubMed14528294
UniProtQ53176|NAPA_CERS4 Periplasmic nitrate reductase (Gene Name=napA)

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