Structure of PDB 1r9t Chain B Binding Site BS04

Receptor Information

>1r9t Chain B (length=1106) Species: 4932 (Saccharomyces cerevisiae)

DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR
TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPC
VEDGFVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLEGFESRKAF
FLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTK
DIFRYMQRTVELAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLN
RYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLS
LMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVH
RNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV
EDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEE
SILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPSMILGVAASI
IPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGT
TRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLF
FRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRV
SGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRV
RTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIP
SRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRG
FEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQP
VEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGL
MTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYT
DRSRDF

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 1r9t Chain B Residue 1308

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1r9t Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): R766 K987 S1019
• Binding residue (residue number reindexed from 1): R661 K869 S901
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D837
• Catalytic site (residue number reindexed from 1): D732
• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

Gene Ontology

Molecular Function

• GO:0001055 RNA polymerase II activity
• GO:0003677 DNA binding
• GO:0003729 mRNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0032549 ribonucleoside binding
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0001172 RNA-templated transcription
• GO:0006351 DNA-templated transcription
• GO:0006366 transcription by RNA polymerase II
• GO:0006367 transcription initiation at RNA polymerase II promoter
• GO:0006368 transcription elongation by RNA polymerase II

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005665 RNA polymerase II, core complex
• GO:0005739 mitochondrion
• GO:0010494 cytoplasmic stress granule

External links

• PDB: RCSB:1r9t, PDBe:1r9t, PDBj:1r9t
• PDBsum: 1r9t
• PubMed: 15537538
• UniProt: P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)