Structure of PDB 1nml Chain A Binding Site BS01

Receptor Information
>1nml Chain A (length=316) Species: 2743 (Marinobacter nauticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DNLMERANSMFEPIPKYPPVIDGNELTQAKVELGKMEFFEPRLSSSHLIS
CNTCHNVGLGGDDELPTSIGHGWQKGPRNSPTVFNAVFNAAQFWDGRAAD
LAEQAKGPVQAGVEMSSTPDRVVATLKSMPEYIERFEDAFPGQENPVTFD
NMAVAIEAYEATLITPEAPFDKYLRGDTSALNESEKEGLALFMDRGCTAC
HSGVNLGGQNYYPFGLVAKKGRFSVTETASDEYVFRASPLRNIELTAPYF
HSGAVWSLEEAVAVMGTAQLGTELNNDEVKSIVAFLKTLTGNVPEVTYPV
LPPSTANTPKPVDMIP
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 chain1nml Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1nml Structural basis for the mechanism of Ca(2+) activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617
Resolution2.2 Å
Binding residue
(original residue number in PDB)		C51 C54 H55 I69 H71 R78 S80 P81 Q92 F93 P108 G112 E160 R246
Binding residue
(residue number reindexed from 1)		C51 C54 H55 I69 H71 R78 S80 P81 Q92 F93 P108 G112 E160 R236
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E114
Catalytic site (residue number reindexed from 1) E114
Enzyme Commision number 1.11.1.5: cytochrome-c peroxidase.
Gene Ontology
Molecular Function
GO:0004130 cytochrome-c peroxidase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1nml, PDBe:1nml, PDBj:1nml
PDBsum1nml
PubMed15274917
UniProtP83787

[Back to BioLiP]