Structure of PDB 7rdq Chain D Binding Site BS02

Receptor Information
>7rdq Chain D (length=1366) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQL
LTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV
ALYRFPRRVRVEYVKKEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAI
DPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVL
ADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLE
ALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLP
PDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEK
RMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGK
RVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVK
AARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLV
EGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLS
PASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEV
ALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGK
RLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLR
LGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKL
LQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLY
VMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYF
ISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVP
LFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDV
HLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAV
GIVAAQSIGEPGTQLTTQGLPRVIELFEARRPKAKAVISEIDGVVRIEET
EEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLL
EAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGD
SRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLS
AASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQV
VDQKTLKAIEEARKEA
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 chain7rdq Chain D Residue 2001 [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]
PDB7rdq Structural and mechanistic basis of reiterative transcription initiation.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		C1112 C1194 C1204
Binding residue
(residue number reindexed from 1)		C991 C1073 C1083
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
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:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7rdq, PDBe:7rdq, PDBj:7rdq
PDBsum7rdq
PubMed35082149
UniProtQ8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]