Structure of PDB 1r5u Chain A Binding Site BS01

Receptor Information
>1r5u Chain A (length=1380) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIG
GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKK
VCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETD
VPSLVSRGGCGNTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHISVKDF
TSLGFNEVFSRPEWMILTCLPVPPPPVRPSEDDLTFKLADILKANISLET
LEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQAPVKSIRARLKGKEG
RIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYN
IDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVER
HIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDG
DEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKL
TLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPN
GIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVT
REKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIA
EAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAE
VNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTL
PHFSKDDYSPESKGFVENSYLRGLPQEFFFHAMGGREGLIDTAVKTAETG
YIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDT
IGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQ
LVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKD
IVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEY
RLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLKKVT
SGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKS
VTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQQSPWLLRLELDRAAMNDK
DLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVAEEDHMLKKIEN
TMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSE
VMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNY
RHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGAS
AELDDCRGVSENVILGQMAPIGTGAFDVMI
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain1r5u Chain A Residue 1735 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1r5u Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms.
Resolution4.5 Å
Binding residue
(original residue number in PDB)		C67 C70 H80
Binding residue
(residue number reindexed from 1)		C66 C69 H79
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485
Catalytic site (residue number reindexed from 1) D447 D449 D451
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

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1r5u, PDBe:1r5u, PDBj:1r5u
PDBsum1r5u
PubMed14963322
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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