Structure of PDB 7x3t Chain V Binding Site BS03

Receptor Information

>7x3t Chain V (length=792) Species: 559292 (Saccharomyces cerevisiae S288C)

DLEGTTKRFEHLLSLSGLFKHFIESKADPKFRQVLDVLEENQFRESPAYV
NGQLRPYQIQGVNWLVSLHKNKIAGILADEMGLGKTLQTISFLGYLRYIE
KIPGPFLVIAPKSTLNNWLREINRWTPDVNAFILQGDKEERAELIQKKLL
GCDFDVVIASYEIIIREKSPLKKINWEYIIIDEAHRIKNEESMLSQVLRE
FTSRNRLLITGTPLQNNLHELWALLNFLLPDIFSDAQDFDDWFSSESTEE
DQDKIVKQLHTVLQPFLLRRIKSDVETSLLPKKELNLYVGMSSMQKKWYK
KILEKDESKTRLLNIMMQLRKCCNHPYLFDGAEPGPPYTTDEHLVYNAAK
LQVLDKLLKKLKEEGSRVLIFSQMSRLLDILEDYCYFRNYEYCRIDGSTA
HEDRIQAIDDYNAPDSKKFVFLLTTRAGGLGINLTSADVVVLYDSDWNPQ
ADLQAMDRAHRIGQKKQVKVFRLVTDNSVEEKILERATQKLRLDQLVIQQ
NRTSNPTKRERHPRMPKPHVFHSHQLQPPQLKVLYEKERMWTAKKTGYVP
TMDDVKAAYGDISDEEEKKQKLELLKLSVNNSQPLTEEEEKMKADWESEG
FTNWNKLEFRKFITVSGKYGRNSIQAIARELAPGKTLEEVRAYAKAFWSN
IERIEDYEKYLKIIENEEEKIKRVKMQQEALRRKLSEYKNPFFDLKLKHP
PSSNNKRTYSEEEDRFILLMLFKYGLDRDDVYELVRDEIRDCPLFELDFY
FRSRTPVELARRGNTLLQCLEKEFNAGIVLDDATKDRMKKED

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: 7x3t Chain V Residue 1201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7x3t ISW1a-dinucleosome
• Resolution: 5.4 Å
• Binding residue (original residue number in PDB): Q195 R197 Q200 G224 G226 K227 T228 L229 E263 W267 R614 I615
• Binding residue (residue number reindexed from 1): Q53 R55 Q58 G82 G84 K85 T86 L87 E121 W125 R461 I462
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.6.4.-

Gene Ontology

Molecular Function

• GO:0000182 rDNA binding
• GO:0000976 transcription cis-regulatory region binding
• GO:0003677 DNA binding
• GO:0003730 mRNA 3'-UTR binding
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008094 ATP-dependent activity, acting on DNA
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0031491 nucleosome binding
• GO:0140658 ATP-dependent chromatin remodeler activity

Biological Process

• GO:0001178 regulation of transcriptional start site selection at RNA polymerase II promoter
• GO:0006325 chromatin organization
• GO:0006338 chromatin remodeling
• GO:0006354 DNA-templated transcription elongation
• GO:0006355 regulation of DNA-templated transcription
• GO:0006363 termination of RNA polymerase I transcription
• GO:0006369 termination of RNA polymerase II transcription
• GO:0007062 sister chromatid cohesion
• GO:0009408 response to heat
• GO:0045944 positive regulation of transcription by RNA polymerase II
• GO:0046832 negative regulation of RNA export from nucleus
• GO:1902275 regulation of chromatin organization
• GO:1903895 negative regulation of IRE1-mediated unfolded protein response

Cellular Component

• GO:0005634 nucleus
• GO:0016587 Isw1 complex
• GO:0030874 nucleolar chromatin
• GO:0036436 Isw1a complex
• GO:0036437 Isw1b complex

External links

• PDB: RCSB:7x3t, PDBe:7x3t, PDBj:7x3t
• PDBsum: 7x3t
• PubMed: 38177688
• UniProt: P38144|ISW1_YEAST ISWI chromatin-remodeling complex ATPase ISW1 (Gene Name=ISW1)