Structure of PDB 1k83 Chain A Binding Site BS04

Receptor Information
>1k83 Chain A (length=1366) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPEKIGGLNDPRLGSIDR
NLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKL
LLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVS
RGGCGNTQPTIRKDGLKLVGSWKKEPELRVLSTEEILNIFKHISVKDFTS
LGFNEVFSRPEWMILTCLPVPPPPVRDDLTFKLADILKANISLETLEHNG
APHHAIEEAESLLQFHVATYMDNDIAGQSIRARLKGKEGRIVDFSARTVI
SGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAK
YVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKM
SMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQ
LCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWV
PDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDN
GMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVV
NFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLT
AKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKG
SFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENS
YLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYD
NTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLN
TDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEAN
WPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGK
NEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQF
LRSVVHPGEMVGVLAAQSIGEPATQMTLKKVTSGVPRLKEILNVAKNMKT
PSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVI
PEDEEIIQLHFSQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDL
FVIWSEDNDEKLIIRCRVVAEEDHMLKKIENTMLENITLRGVENIERVVM
MKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFID
IMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSV
TRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMA
PIGTGAFDVMIDEESL
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain1k83 Chain A Residue 3009 [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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PDB1k83 Structural Basis of Transcription: Alpha-Amanitin-RNA Polymerase II Cocrystal at 2.8 A Resolution.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D481 D483 D485
Binding residue
(residue number reindexed from 1)		D428 D430 D432
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485
Catalytic site (residue number reindexed from 1) D428 D430 D432
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:1k83, PDBe:1k83, PDBj:1k83
PDBsum1k83
PubMed11805306
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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