Structure of PDB 7nkz Chain A Binding Site BS03

Receptor Information

>7nkz Chain A (length=455) Species: 83332 (Mycobacterium tuberculosis H37Rv)

MNVVDISRWQFGITTVYHFIFVPLTIGLAPLIAVMQTLWVVTDNPAWYRL
TKFFGKLFLINFAIGVATGIVQEFQFGMNWSEYSRFVGDVFGAPLAMEGL
AAFFFESTFIGLWIFGWNRLPRLVHLACIWIVAIAVNVSAFFIIAANSFM
QHPVGAHYNPTTGRAELSSIVVLLTNNTAQAAFTHTVSGALLTAGTFVAA
VSAWWLVRSSTDTQAMYRPATILGCWVALAATAGLLFTGDHQGKLMFQQQ
PMKMASAESLCDTQTDPNFSVLTVGRQNNCDSLTRVIEVPYVLPFLAEGR
ISGVTLQGIRDLQQEYQQRFGPNDYRPNLFVTYWSFRMMIGLMAIPVLFA
LIALWLTRGGQIPNQRWFSWLALLTMPAPFLANSAGWVFTEMGRQPWVVV
PNPTGDQLVRLTVKAGVSDHSATVVATSLLMFTLVYAVLAVIWCWLLKRY
IVEGP

Ligand information

• Ligand ID: HDD
• InChI: InChI=1S/C34H32N4O5.Fe/c1-7-20-17(3)23-13-24-19(5)22(9-10-31(39)40)28(37-24)16-30-34(12-11-32(41)43-34)33(6,42)29(38-30)15-27-21(8-2)18(4)25(36-27)14-26(20)35-23;/h7-8,13-16,42H,1-2,9-12H2,3-6H3,(H,39,40);/q-4;+4/b23-13-,26-14-,29-15-,30-16-;/t33-,34+;/m0./s1
• InChIKey: UMGOPAWIGKFTRK-QQDQPIDJSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1c2n3c(c1CCC(=O)O)C=C4[C@]5(CCC(=O)O5)[C@@](C6=Cc7c(c(c8n7[Fe]3(N64)N9C(=C2)C(=C(C9=C8)C=C)C)C)C=C)(C)O
  CACTVS 3.341: Cc1c(CCC(O)=O)c2C=C3N4C(=Cc5n6c(C=C7N8C(=Cc1n2[Fe]468)C(=C7C=C)C)c(C)c5C=C)[C](C)(O)[C]39CCC(=O)O9
  CACTVS 3.341: Cc1c(CCC(O)=O)c2C=C3N4C(=Cc5n6c(C=C7N8C(=Cc1n2[Fe@]468)C(=C7C=C)C)c(C)c5C=C)[C@](C)(O)[C@@]39CCC(=O)O9
  ACDLabs 10.04: O=C(O)CCc1c(c2C=C7C(=C(\C=C)C6=Cc5c(c(\C=C)c4C=C9N3C(=Cc1n2[Fe]3(n45)N67)C8(OC(=O)CC8)C9(O)C)C)C)C
  OpenEye OEToolkits 1.5.0: Cc1c2n3c(c1CCC(=O)O)C=C4C5(CCC(=O)O5)C(C6=Cc7c(c(c8n7[Fe]3(N64)N9C(=C2)C(=C(C9=C8)C=C)C)C)C=C)(C)O
• Formula: C34 H32 Fe N4 O5
• Name: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE;
  HEME
• PDB chain: 7nkz Chain A Residue 703

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7nkz The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): H18 V22 I26 F62 V66 G69 Q72 E73 F76 F103 E106 S107 S139 A140 I143
• Binding residue (residue number reindexed from 1): H18 V22 I26 F62 V66 G69 Q72 E73 F76 F103 E106 S107 S139 A140 I143
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0009055 electron transfer activity
• GO:0016682 oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
• GO:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0019646 aerobic electron transport chain

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0070069 cytochrome complex

External links

• PDB: RCSB:7nkz, PDBe:7nkz, PDBj:7nkz
• PDBsum: 7nkz
• PubMed: 34475399
• UniProt: L7N662