Structure of PDB 3fki Chain A

Receptor sequence
>3fkiA (length=1427) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIG
GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKK
VCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETD
VPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRV
LSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSIS
FNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVA
TYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSART
VISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG
AKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLH
KMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAEL
SQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLY
WVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPK
DNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQK
VVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANL
LTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGS
KGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVE
NSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVH
YDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDL
LNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGE
ANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLR
GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEA
QFLRSVVHPGEMVGVLAAQSIGEPATQMTLSKKVTSGVPRLKEILNVAKN
MKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRS
TVIPEDEEIIQLHFSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQT
FKNDLFVIWSEDNDEKLIIRCRVVRPAEEDHMLKKIENTMLENITLRGVE
NIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRI
YTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTT
QGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSEN
VILGQMAPIGTGAFDVMIDEESLVKYM
3D structure
PDB3fki Structure of the 12-Subunit RNA Polymerase II Refined with the Aid of Anomalous Diffraction Data
ChainA
Resolution3.88 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485
Catalytic site (residue number reindexed from 1) D480 D482 D484
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ZN A C110 C148 C167 C109 C147 C166
BS02 ZN A C67 C70 H80 C66 C69 H79
BS03 MG A D481 D483 D480 D482
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:3fki, PDBe:3fki, PDBj:3fki
PDBsum3fki
PubMed19289466
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

[Back to BioLiP]