Structure of PDB 6vd3 Chain B Binding Site BS01

Receptor Information

>6vd3 Chain B (length=137) Species: 129555 (Amphitrite ornata)

GFKQDIATLRGDLRTYAQDIFLAFLNKYPDEKRNFKNYVGKSDQELKSMA
KFGDHTEKVFNLMMEVADRATDCVPLASDASTLVQMKQHSGLTTGNFEKL
FVALVEYMRASGQSFDSQSWDRFGKNLVSALSSAGMK

Ligand information

• Ligand ID: MH0
• InChI: InChI=1S/C34H36N4O4.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;/h13-16H,7-12H2,1-6H3,(H,39,40)(H,41,42);/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
• InChIKey: CKMCSMAXNUVLQI-RGGAHWMASA-N
• SMILES:
  CACTVS 3.370: [Fe]|1|2|3|N4=C5C=C6N|1=C(C=C7N|2=C(C=C8N|3=C(C=C4C(=C5CC)C)C(=C8CCC(O)=O)C)C(=C7C)CCC(O)=O)C(=C6C)CC
  OpenEye OEToolkits 1.7.6: CCC1=C(C2=CC3=[N]4C(=CC5=[N]6[Fe]47[N]2=C1C=C8[N]7=C(C=C6C(=C5CCC(=O)O)C)C(=C8C)CC)C(=C3C)CCC(=O)O)C
  ACDLabs 12.01: O=C(O)CCC1=C(C2=CC=6C(=C(C5=CC=4C(=C(C3=CC=7C(=C(C8=CC1=N2[Fe](N3=4)(N5=6)N=78)CCC(=O)O)C)C)CC)C)CC)C
• Formula: C34 H36 Fe N4 O4
• Name: Mesoheme
• PDB chain: 6vd3 Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vd3 Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): F24 H55 K58 V59 L62 M63 L83 M86 Q88 H89 L92 N96 F97
• Binding residue (residue number reindexed from 1): F24 H55 K58 V59 L62 M63 L83 M86 Q88 H89 L92 N96 F97
• Annotation score: 1

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:6vd3, PDBe:6vd3, PDBj:6vd3
• PDBsum: 6vd3
• UniProt: Q9NAV7