Structure of PDB 3o7n Chain B Binding Site BS01

Receptor Information

>3o7n Chain B (length=137) Species: 129555 (Amphitrite ornata)

GFKQDIATIRGDLRTYAQDIFLAFLNKYPDERRYFKNYVGKSDQELKSMA
KFGDHTEKWFNLMMEVADRATDCVPLASDANTLVQMKQHSSLTTGNFEKL
FVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK

Ligand information

• Ligand ID: HEM
• InChI: InChI=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,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
• InChIKey: KABFMIBPWCXCRK-RGGAHWMASA-L
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
  CACTVS 3.385: CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
  ACDLabs 12.01: C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
• Formula: C34 H32 Fe N4 O4
• Name: PROTOPORPHYRIN IX CONTAINING FE;
  HEME
• DrugBank: DB18267
• PDB chain: 3o7n Chain B Residue 139

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3o7n The V59W mutation blocks the distal pocket of the hemoglobin - dehaloperoxidase from Amphitirite ornata
• Resolution: 1.72 Å
• Binding residue (original residue number in PDB): F24 F35 H55 K58 W59 M63 L83 M86 Q88 H89 L92 N96 F97
• Binding residue (residue number reindexed from 1): F24 F35 H55 K58 W59 M63 L83 M86 Q88 H89 L92 N96 F97
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0004601 peroxidase activity
• GO:0005344 oxygen carrier activity
• GO:0019825 oxygen binding
• GO:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0015671 oxygen transport
• GO:0098869 cellular oxidant detoxification

External links

• PDB: RCSB:3o7n, PDBe:3o7n, PDBj:3o7n
• PDBsum: 3o7n
• UniProt: Q9NAV8