Structure of PDB 6vdr Chain B Binding Site BS01

Receptor Information

>6vdr Chain B (length=137) Species: 129555 (Amphitrite ornata)

GFKQDIATLRGDLRTYAQDIFLAFLNKYPDEKRNFKNYVGKSDQELKSMA
KFGDHTEKVFNLMMEVADRATDCVPLASDASTLVQMKQHSGLTTGNFEKL
FVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK

Ligand information

• Ligand ID: FDE
• InChI: InChI=1S/C30H30N4O4.Fe/c1-15-9-20-12-25-17(3)21(5-7-29(35)36)27(33-25)14-28-22(6-8-30(37)38)18(4)26(34-28)13-24-16(2)10-19(32-24)11-23(15)31-20;/h9-14H,5-8H2,1-4H3,(H4,31,32,33,34,35,36,37,38);/q;+2/p-2/b19-11-,20-12-,23-11-,24-13-,25-12-,26-13-,27-14-,28-14-;
• InChIKey: QQYZTXBVPVYDJC-RWRCOHKGSA-L
• SMILES:
  CACTVS 3.385: CC1=CC2=Cc3n4[Fe][N]5C(=CC1=N2)C(=C(CCC(O)=O)C5=CC6=NC(=Cc4cc3C)C(=C6CCC(O)=O)C)C
  OpenEye OEToolkits 2.0.7: Cc1cc2n3c1C=C4C=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8CCC(=O)O)C)C(=C(C7=C2)C)CCC(=O)O)C
  CACTVS 3.385: CC1=CC2=Cc3n4[Fe][N@@]5C(=CC1=N2)C(=C(CCC(O)=O)C5=CC6=NC(=Cc4cc3C)C(=C6CCC(O)=O)C)C
• Formula: C30 H28 Fe N4 O4
• Name: FE(III) DEUTEROPORPHYRIN IX
• PDB chain: 6vdr Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vdr Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme
• Resolution: 1.87 Å
• Binding residue (original residue number in PDB): N34 F35 K36 K51 H55 V59 M86 H89 F97
• Binding residue (residue number reindexed from 1): N34 F35 K36 K51 H55 V59 M86 H89 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:6vdr, PDBe:6vdr, PDBj:6vdr
• PDBsum: 6vdr
• UniProt: Q9NAV7