Structure of PDB 6v11 Chain B Binding Site BS01

Receptor Information

>6v11 Chain B (length=496) Species: 632 (Yersinia pestis)

ALKRKIEAAKMPKDAREKTEAELQKLKMMSPMSAEATVVRGYIDWMLQVP
WNSRSKVKKDLVKAQEVLDTDHYGLERVKDRILEYLAVQSRVSKIKGPIL
CLVGPPGVGKTSLGQSIAKATGRQYVRMALGGKLIQKMAKVGVKNPLFLL
DEIDKMAPASALLEVLDPEQNVAFNHYLEVDYDLSDVMFVATSNSMNIPA
PLLDRMEVIRLSGYTEDEKLNIAKQHLLPKQFERNAIKKGELTIDDSAIM
SIIRYYTREAGVRSLEREISKLCRKAVKNLLMDKTVKHIEINGDNLKDFL
GVQKVDYGRADTENRVGQVTGLAWTEVGGDLLTIETACVPGKGKLTYTGS
LGEVMQESIQAALTVVRARADKLGINPDFYEKRDIHVHVPEGATPKDGPS
AGIAMCTALVSCLTGNPVRADVAMTGEITLRGLVLPIGGLKEKLLAAHRG
GIKVVLIPDDNKRDLEEIPDNVIADLEIHPVKRIDDVLAIALEHPA

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: 6v11 Chain B Residue 800

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6v11 Structural basis for distinct operational modes and protease activation in AAA+ protease Lon.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): D323 H324 Y325 G359 V360 G361 K362 T363 Y493 R542
• Binding residue (residue number reindexed from 1): D71 H72 Y73 G107 V108 G109 K110 T111 Y214 R263
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.4.21.53: endopeptidase La.

Gene Ontology

Molecular Function

• GO:0004176 ATP-dependent peptidase activity
• GO:0004252 serine-type endopeptidase activity
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0006508 proteolysis
• GO:0030163 protein catabolic process

External links

• PDB: RCSB:6v11, PDBe:6v11, PDBj:6v11
• PDBsum: 6v11
• PubMed: 32490208
• UniProt: A0A5P8YJ65