Structure of PDB 7kef Chain A Binding Site BS07

Receptor Information

>7kef Chain A (length=1390) Species: 559292 (Saccharomyces cerevisiae S288C)

GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCELVS
RGGCGNTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHISVKDFTSLGFN
EVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANIS
LETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSI
RARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLT
YPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQ
LQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVT
SPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQ
DTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGK
QILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSS
NGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPT
MREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEA
RDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRI
AFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLI
DTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDA
AHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKL
QVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDH
TKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSR
LATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEP
ATQMTLKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIR
SAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQQSPWLLRL
ELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVAE
EDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWV
LETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNV
IASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEET
VEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMI

Ligand information

• Ligand ID: WC4
• InChI: InChI=1S/C16H19O8P/c1-22-12-7-10-5-3-2-4-9(10)6-11(12)16-15(18)14(17)13(24-16)8-23-25(19,20)21/h2-7,13-18H,8H2,1H3,(H2,19,20,21)/t13-,14-,15-,16+/m1/s1
• InChIKey: JKJYMBPWCSVIAM-FPCVCCKLSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: COc1cc2ccccc2cc1C3C(C(C(O3)COP(=O)(O)O)O)O
  CACTVS 3.385: COc1cc2ccccc2cc1[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  ACDLabs 12.01: COc3c(C1C(C(C(COP(O)(=O)O)O1)O)O)cc2c(cccc2)c3
  OpenEye OEToolkits 2.0.7: COc1cc2ccccc2cc1C3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O
  CACTVS 3.385: COc1cc2ccccc2cc1[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
• Formula: C16 H19 O8 P
• Name: (1S)-1,4-anhydro-1-(3-methoxynaphthalen-2-yl)-5-O-phosphono-D-ribitol
• PDB chain: 7kef Chain R Residue 11

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7kef Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.
• Resolution: 3.89 Å
• Binding residue (original residue number in PDB): N479 D483 D485
• Binding residue (residue number reindexed from 1): N454 D458 D460
• Annotation score: 1

Enzymatic activity

• 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: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: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
• GO:0019985 translesion synthesis

Cellular Component

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

External links

• PDB: RCSB:7kef, PDBe:7kef, PDBj:7kef
• PDBsum: 7kef
• PubMed: 34140682
• UniProt: P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)