Structure of PDB 5m3m Chain B Binding Site BS01

Receptor Information
>5m3m Chain B (length=1166) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TADFRTLERESRFINPPKDKSAFPLLQEAVQPHIGSFNALTEGPDGGLLN
LGVKDIGEKVIFDGKPLNSGYLGNKLSVSVEQVSIAKPMSNDGVSSAVER
KVYPSESRQRLTSYRGKLLLKLKWSVNNGEENLFEVRDCGGLPVMLQSNR
CHLNKMSPYELVQHKEESDEIGGYFIVNGIEKLIRMLIVQRRNHPMAIIR
PSFANRGASYSHYGIQIRSVRPDQTSQTNVLHYLNDGQVTFRFSWRKNEY
LVPVVMILKALCHTSDREIFDGIIGNDVKDSFLTDRLELLLRGFKKRYPH
LQNRTQVLQYLGDKFRVVFQASPDQSDLEVGQEVLDRIVLVHLGKDGSQD
KFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVLLGGFLYGMILKEKIDE
YLQNIIAQVRMDINRGMAINFKDKRYMSRVLMRVNENIGSKMQYFLSTGN
LVSQSGLDLQQVSGYTVVAEKINFYRFISHFRMVHRGSFFAQLKTTTVRK
LLPESWGFLCPVHTPDGSPCGLLNHFAHKCRISTQQSDVSRIPSILYSLG
VAPASHTFAAGPSLCCVQIDGKIIGWVSHEQGKIIADTLRYWKVEGKTPG
LPIDLEIGYVPPSTRGQYPGLYLFGGHSRMLRPVRYLPLDKEDIVGPFEQ
VYMNIAVTPQEIQNNVHTHVEFTPTNILSILANLTPFSDFNQSPRNMYQC
QMGKQTMGTPGVALCHRSDNKLYRLQTGQTPIVKANLYDDYGMDNFPNGF
NAVVAVISYTGYDMDDAMIINKSADERGFGYGTMYKTEKVDLALNRNRGD
PITQHFGFGNDEWPKEWLEKLDEDGLPYIGTYVEEGDPICAYFDDTLNKT
KIKTYHSSEPAYIEEVNLIGDESNKFQELQTVSIKYRIRRTPQIGDKFSS
RHGQKGVCSRKWPTIDMPFSETGIQPDIIINPHAFPSRMTIGMFVESLAG
KAGALHGIAQDSTPWIFNEDDTPADYFGEQLAKAGYNYHGNEPMYSGATG
EELRADIYVGVVYYQRLRHMVNDKFQVRSTGPVNSLTMQPVKIRVGEMER
DALIGHGTSFLLQDRLLNSSDYTQASVCRECGSILTTQQSVPRIGSISTV
CCRRCSMRFEDAKIFIDDSQIWEDGQGNKFVGGNETTTVAIPFVLKYLDS
ELSAMGIRLRYNVEPK
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 chain5m3m Chain B Residue 1302 [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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PDB5m3m Structure of RNA polymerase I transcribing ribosomal DNA genes.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		C1104 R1105 E1106 E1172
Binding residue
(residue number reindexed from 1)		C1078 R1079 E1080 E1135
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5m3m, PDBe:5m3m, PDBj:5m3m
PDBsum5m3m
PubMed27842382
UniProtP22138|RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135 (Gene Name=RPA135)

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