Structure of PDB 5obo Chain A Binding Site BS03

Receptor Information
>5obo Chain A (length=456) Species: 658080 (Ralstonia sp. 5_2_56FAA) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLPGDFGPPRGEPIHAVLTSPPLVPPPVNRTYPAKVIVELEVVEKEMQIS
EGVSYTFWTFGGTVPGSFIRVRQGDTVEFHLKNHPSSKMPHNINLHGVTG
PGGGAASSFTAPGHESQFTFKALNEGIYVYHCATAPVGMHIANGMYGLIL
VEPPEGLPKVDHEYYVMQGDFYTAGKYREKGLQPFDMEKAIDERPSYVLF
NGAEGALTGDKALHAKVGETVRIFVGNGGPNLVSSFHVIGAIFDQVRYEG
GTNVQKNVQTTLIPAGGAAVVKFTARVPGSYVLVDHSIFRAFNKGAMAIL
KIDGAENKLVYSGKELDSVYLGDRAAPNMSAVTKATQASVSGTLTVQDQV
QAGRALFAGTCSVCHQGNGAGLPGVFPPLAKSDFLAADPKRAMNIVLHGL
NGKIKVNGQEYDSVMPPMTQLNDDEVANILTYVLNSWDNPGGRVSAEDVK
KVRAQP
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 chain5obo Chain A Residue 503 [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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PDB5obo Activation of redox tyrosine switch is required for ligand binding at the catalytic site in heme-cu nitrite reductases
Resolution1.89 Å
Binding residue
(original residue number in PDB)		T363 C364 C367 H368 P380 P381 L382 S385 F387 I398 N404 G405 S416 M418 M421
Binding residue
(residue number reindexed from 1)		T360 C361 C364 H365 P377 P378 L379 S382 F384 I395 N401 G402 S413 M415 M418
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H94 N97 H99 H134 C135 H143 M148 H240 Q262 T263 H289
Catalytic site (residue number reindexed from 1) H91 N94 H96 H131 C132 H140 M145 H237 Q259 T260 H286
Enzyme Commision number 1.7.2.1: nitrite reductase (NO-forming).
Gene Ontology
Molecular Function
GO:0005507 copper ion binding
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0050421 nitrite reductase (NO-forming) activity
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:5obo, PDBe:5obo, PDBj:5obo
PDBsum5obo
PubMed
UniProtU3G913

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