Structure of PDB 4by1 Chain A Binding Site BS01

Receptor Information
>4by1 Chain A (length=1427) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIG
GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKK
VCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETD
VPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKDEPELRVLSTEEILN
IFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGE
DDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIA
GQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNL
ELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDS
GDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHR
VKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPL
QIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGV
IPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIID
GQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLH
NGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMT
LRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIA
QMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLT
PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNS
LGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLD
PSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVN
IRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQN
AQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVH
PGEMVGVLAAQSIGEPATQMTLNTVTSGVPRLKEILNVAKNMKTPSLTVY
LEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEI
IQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQT
FKNDLFVIWSEDNDEKLIIRCRVVRAEEDHMLKKIENTMLENITLRGVEN
IERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIY
TNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQ
GGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENV
ILGQMAPIGTGAFDVMIDEESLVKYMP
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4by1 Structures of RNA Polymerase II Complexes with Bye1, a Chromatin-Binding Phf3/Dido1 Homologue
Resolution3.6 Å
Binding residue
(original residue number in PDB)		K101 A1108
Binding residue
(residue number reindexed from 1)		K100 A1089
Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485
Catalytic site (residue number reindexed from 1) D472 D474 D476
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4by1, PDBe:4by1, PDBj:4by1
PDBsum4by1
PubMed24003114
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

[Back to BioLiP]