Structure of PDB 4ybn Chain A Binding Site BS02

Receptor Information

>4ybn Chain A (length=214) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

STRVTRLDEKQSTSRERLDDLLDTIPLATVALVRDGHPVAFPIGFGRVGD
ELVIHGSTGSPWLRALAEGAPAAVSVTALDGVVVARSSFESSFRYRSATL
FGTFEVIADDAKRGYLDALTDRFIPGRTAELRASTRKELAATLALALAIG
DDNWSLKLSEGWPDDADEDIAAGGWAGVVPLTTQYGAPLTAPDVAAGTPL
PPSVRGMTGELRNT

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: 4ybn Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ybn Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): R14 L15 K18 S96 F97 S99 S100 F101 Y103 K165
• Binding residue (residue number reindexed from 1): R6 L7 K10 S88 F89 S91 S92 F93 Y95 K157
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0046872 metal ion binding

External links

• PDB: RCSB:4ybn, PDBe:4ybn, PDBj:4ybn
• PDBsum: 4ybn
• PubMed: 26434506
• UniProt: A0R238