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Structure of PDB 7w3c Chain F Binding Site BS01

Receptor Information

>7w3c Chain F (length=395) Species: 9606 (Homo sapiens)

EQDGIGEEVLKMSTEEIIQRTRLLDSEIKIMKSEVLRVTHELQAMKDKIK
ENSEKIKVNKTLPYLVSNVIELLDVKCAVIKTSTRQTYFLPVIGLVDAEK
LKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDERPTEQYSDIGGLDKQ
IQELVEAIVLPMNHKEKFENLGIQPPKGVLMYGPPGTGKTLLARACAAQT
KATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPSIIFIDELDAIGTK
RFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLR
SGRLDRKIEFPMPNEEARARIMQIHSRKMNVSPDVNYEELARCTDDFNGA
QCKAVCVEAGMIALRRGATELTHEDYMEGILEVQAKKKANLQYYA

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: 7w3c Chain F Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7w3c USP14-regulated allostery of the human proteasome by time-resolved cryo-EM.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): G230 T231 G232 T234 L235 I365 H369 G393
• Binding residue (residue number reindexed from 1): G186 T187 G188 T190 L191 I321 H325 G349
• Annotation score: 5

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016887 ATP hydrolysis activity
• GO:0036402 proteasome-activating activity
• GO:0042802 identical protein binding

Biological Process

• GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
• GO:0043921 modulation by host of viral transcription
• GO:0045944 positive regulation of transcription by RNA polymerase II
• GO:1901800 positive regulation of proteasomal protein catabolic process

Cellular Component

• GO:0000502 proteasome complex
• GO:0000932 P-body
• GO:0005576 extracellular region
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0008540 proteasome regulatory particle, base subcomplex
• GO:0016020 membrane
• GO:0022624 proteasome accessory complex
• GO:0034774 secretory granule lumen
• GO:1904813 ficolin-1-rich granule lumen

External links

• PDB: RCSB:7w3c, PDBe:7w3c, PDBj:7w3c
• PDBsum: 7w3c
• PubMed: 35477760
• UniProt: P17980|PRS6A_HUMAN 26S proteasome regulatory subunit 6A (Gene Name=PSMC3)

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