Structure of PDB 8gm3 Chain A Binding Site BS01

Receptor Information

>8gm3 Chain A (length=218) Species: 669 (Vibrio harveyi)

GFDGAISDDSLRQVGESEVWVPFIHSKGNAGIGKTGGKRVDFEGLAGGIF
DDERNGVHTSGSKHFQDNFYSFVQVANQDVWFGEWYEGKKDSEFNNRTVY
YVGNDAGTTVPTSGKATYNITGINKFSGANKLSGTFNADFGAKTLDGSIN
NSNLTVSVDATINAATAAFNGTAQAVQNGTTTNGASQGHFFGANAAGLAG
IATFTNNSDLDTAFGGEK

Ligand information

• Ligand ID: HEB
• 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;/h8,13-16H,2,7,9-12H2,1,3-6H3,(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: NEGHHAJBRZGUAY-RGGAHWMASA-L
• SMILES:
  CACTVS 3.385: CCC1=C(C)C2=NC1=Cc3n4[Fe][N]5C(=C2)C(=C(CCC(O)=O)C5=CC6=NC(=Cc4c(C=C)c3C)C(=C6CCC(O)=O)C)C
  CACTVS 3.385: CCC1=C(C)C2=NC1=Cc3n4[Fe][N@@]5C(=C2)C(=C(CCC(O)=O)C5=CC6=NC(=Cc4c(C=C)c3C)C(=C6CCC(O)=O)C)C
  OpenEye OEToolkits 2.0.7: CCC1=C(C2=[N]3C1=Cc4c(c(c5n4[Fe]36[N]7=C(C=C8N6C(=C2)C(=C8CCC(=O)O)C)C(=C(C7=C5)C)CCC(=O)O)C=C)C)C
• Formula: C34 H34 Fe N4 O4
• Name: HEME B/C;
  HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)
• PDB chain: 8gm3 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8gm3 Heme Acquisition by Slam-dependent Hemophores in Gram-negative Bacteria
• Resolution: 1.727 Å
• Binding residue (original residue number in PDB): R12 V19 V21 I24 H25 G37 K38 V40 L45 F50 S62 K63 H64 Y70
• Binding residue (residue number reindexed from 1): R12 V19 V21 I24 H25 G37 K38 V40 L45 F50 S62 K63 H64 Y70
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:8gm3, PDBe:8gm3, PDBj:8gm3
• PDBsum: 8gm3
• PubMed: 38814789
• UniProt: A0A3A1PTD6