Structure of PDB 8a8v Chain D Binding Site BS02

Receptor Information

>8a8v Chain D (length=576) Species: 1773 (Mycobacterium tuberculosis)

SLVLDQFGRNLTAAAMEGKLDPVIGREKEIERVMQVLSRRTKNNPVLIGE
PGVGKTAVVEGLAQAIVHGEVPETLKDKQLYTLDLGSLVAGSRYRGDFEE
RLKKVLKEINTRGDIILFIDELHTLVGAGAAEGAIDAASILKPKLARGEL
QTIGATTLDEYRKYIEKDAALERRFQPVQVGEPTVEHTIEILKGLRDRYE
AHHRVSITDAAMVAAATLADRYINDRFLPDKAIDLIDEAGARMRIRRMVA
EVDDEQIAEVLGNWTGIPVFKLTEAETTRLLRMEEELHKRIIGQEDAVKA
VSKAIRRTRAGLKDPKRPSGSFIFAGPSGVGKTELSKALANFLFGDDDAL
IQIDMGEFHDRFTASRLFGAPPGYVGYEEGGQLTEKVRRKPFSVVLFDEI
EKAHQEIYNSLLQVLEDGRLTDGQGRTVDFKNTVLIFTSNLGTDYERMKQ
KVNDELKKHFRPEFLNRIDDIIVFHQLTREEIIRMVDLMISRVAGQLKSK
DMALVLTDAAKALLAKRGFDPVLGARPLRRTIQREIEDQLSEKILFEEVG
PGQVVTVDVDNWDGEGPGEDAVFTFT

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 8a8v Chain D Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8a8v Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action.
• Resolution: 3.34 Å
• Binding residue (original residue number in PDB): P189 V190 I191 G221 K222 T223 I358 L362 P396
• Binding residue (residue number reindexed from 1): P22 V23 I24 G54 K55 T56 I191 L195 P229
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.4.-.-

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0042803 protein homodimerization activity
• GO:0044183 protein folding chaperone

Biological Process

• GO:0006457 protein folding

Cellular Component

• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0009274 peptidoglycan-based cell wall

External links

• PDB: RCSB:8a8v, PDBe:8a8v, PDBj:8a8v
• PDBsum: 8a8v
• PubMed: 36208775
• UniProt: P9WPC9|CLPC1_MYCTU ATP-dependent Clp protease ATP-binding subunit ClpC1 (Gene Name=clpC1)