Structure of PDB 7dvr Chain A Binding Site BS01

Receptor Information

>7dvr Chain A (length=147) Species: 211110 (Streptococcus agalactiae NEM316)

MENPLQKARILVNQLEKYLDRYAKEYDVEHLAGPQGHLVMHLYKHPDKDM
SIKDAEEILHISKSVASNLVKRMEKNGFIAIVPSKTDKRVKYLYLTHLGK
QKATQFEIFLEKLHSTMLAGITKEEIRTTKKVIRTLAKNMAMEDFDS

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: 7dvr Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7dvr Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): L110 H114 M117 L118 K123
• Binding residue (residue number reindexed from 1): L110 H114 M117 L118 K123
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003700 DNA-binding transcription factor activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006355 regulation of DNA-templated transcription

External links

• PDB: RCSB:7dvr, PDBe:7dvr, PDBj:7dvr
• PDBsum: 7dvr
• PubMed: 33850260
• UniProt: Q8E4J9