Structure of PDB 4ym7 Chain BB Binding Site BS01

Receptor Information
>4ym7 Chain BB (length=1153) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADFRTLERESRFINPPKDKSAFPLLQEAVQPHIGSFNALTEGPDGGLLNL
GVKDIGEKVIFDGYLGNKLSVSVEQVSIAKPMSNVERKVYPSESRQRLTS
YRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQSNRCHLNKMSPYELVQ
HKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIRPSFANRGASYSHY
GIQIRSVRPDQTSQTNVLHYLNDGQVTFRFSWRKNEYLVPVVMILKALCH
TSDREIFDGIIGNDVKDSFLTDRLELLLRGFKKRYPHLQNRTQVLQYLGD
KFRVVFQASPDQSDLEVGQEVLDRIVLVHLGKDGSQDKFRMLLFMIRKLY
SLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDEYLQNIIAQVRMDI
NRGMAINFKDKRYMSRVLMRVNENIGSKMQYFLSTGNLVSQSGLDLQQVS
GYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTTVRKLLPESWGFLCPVH
TPDGSPCGLLNHFAHKCRISTQQSDVSRIPSILYSLGVAPASHTFAAGPS
LCCVQIDGKIIGWVSHEQGKIIADTLRYWKVEGKTPGLPIDLEIGYVPPS
TRGQYPGLYLFGGHSRMLRPVRYLPLDKEDIVGPFEQVYMNIAVTPQEIQ
NNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQCQMGKQTMGTPGVA
LCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGFNAVVAVISYTGYD
MDDAMIINKSADERGFGYGTMYKTEKVDLALNPITQHFGFGNDEWPKEWL
EKLDEDGLPYIGTYVEEGDPICAYFDDTLNKTKIKTYHSSEPAYIEEVNL
IGDEFQELQTVSIKYRIRRTPQIGDKFSSRHGQKGVCSRKWPTIDMPFSE
TGIQPDIIINPHAFPSRMTIGMFVESLAGKAGALHGIAQDSTPWIFNEDD
TPADYFGEQLAKAGYNYHGNEPMYSGATGEELRADIYVGVVYYQRLRHMV
NDKFQVRSTGPVNSLTMQPVKGRKRHGGIRVGEMERDALIGHGTSFLLQD
RLLNSSDYTQASVCRECGSILTTQQSVPRIGSISTVCCRRCSMRFEDAKK
LLIDDSQIWEDGQGNKFVGGNETTTVAIPFVLKYLDSELSAMGIRLRYNV
EPK
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 chain4ym7 Chain BB Residue 3001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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]
PDB4ym7 An alternative RNA polymerase I structure reveals a dimer hinge.
Resolution5.5 Å
Binding residue
(original residue number in PDB)		C1104 C1107 C1128 C1131
Binding residue
(residue number reindexed from 1)		C1064 C1067 C1088 C1091
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0001054 RNA polymerase I activity
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0006360 transcription by RNA polymerase I
GO:0006361 transcription initiation at RNA polymerase I promoter
GO:0006362 transcription elongation by RNA polymerase I
GO:0006363 termination of RNA polymerase I transcription
GO:0042254 ribosome biogenesis
GO:0042790 nucleolar large rRNA transcription by RNA polymerase I
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005736 RNA polymerase I complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ym7, PDBe:4ym7, PDBj:4ym7
PDBsum4ym7
PubMed26327374
UniProtP22138|RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135 (Gene Name=RPA135)

[Back to BioLiP]