Structure of PDB 8w3a Chain B Binding Site BS02

Receptor Information

>8w3a Chain B (length=116) Species: 314608 (Shewanella benthica KT99)

SLYERLGGEQKIARIAADIFDTHATNPTVASRYKDSDRERVIKMVTEFLS
AGTGGPQDYTGKSMPEAHRSMNINEAEYLAVIDDIMVALDKNEVGDQEKQ
ELLMIAYSLKGEIIGA

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: 8w3a Chain B Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8w3a Heme D formation in a Shewanella benthica truncated hemoglobin
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): Y34 S37 V42 M45 F49 Y60 G62 K63 M65 H69 M72 I74 Y79 V82 I114
• Binding residue (residue number reindexed from 1): Y33 S36 V41 M44 F48 Y59 G61 K62 M64 H68 M71 I73 Y78 V81 I113
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0019825 oxygen binding
• GO:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0015671 oxygen transport

External links

• PDB: RCSB:8w3a, PDBe:8w3a, PDBj:8w3a
• PDBsum: 8w3a
• PubMed: 38959524
• UniProt: A9DF82