Structure of PDB 4ayb Chain D Binding Site BS01

Receptor Information
>4ayb Chain D (length=262) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SINLLHKDDKRIDLVFEGYPLEFVNAIRRAAMLYVPVMSIDDVYFIENNS
PLYDEILAHRLALIPFTSEEALDTYRWPEECIDCTENCEKCYTKIYIEAE
ALNEPKMLYSKDIKSEDPSIVPISGDIPIVLLGANQKISLEARLRLGYGK
EHAKFIPVSLAIVRYYPKVEILGNCEKGATVCPEGVFELKDGKLSVKNEL
ACTLCEECLRYCNGLIRISSVEDKYILELESVGSLKPERILLEAGKSIIR
KIEELEKKLVEV
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain4ayb Chain D Residue 1264 [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]
PDB4ayb Structural and Functional Analyses of the Interaction of Archaeal RNA Polymerase with DNA.
Resolution3.202 Å
Binding residue
(original residue number in PDB)		C183 E185 V187 F188 C203 C206 E207 C209
Binding residue
(residue number reindexed from 1)		C182 E184 V186 F187 C202 C205 E206 C208
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
GO:0046983 protein dimerization activity
GO:0051536 iron-sulfur cluster binding
GO:0051538 3 iron, 4 sulfur cluster binding
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ayb, PDBe:4ayb, PDBj:4ayb
PDBsum4ayb
PubMed22848102
UniProtB8YB56|RPO3_SACSH DNA-directed RNA polymerase subunit Rpo3 (Gene Name=rpo3)

[Back to BioLiP]