Structure of PDB 5d4d Chain M Binding Site BS01

Receptor Information
>5d4d Chain M (length=1091) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRE
TFPIEGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARDEVFLGHIPL
MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGP
WIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQG
LMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLG
EAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGH
EVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLTPAKLVNSRP
LEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDV
RDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGG
VVTDEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPE
EVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAP
VVMTGLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVEYPLRR
FYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIM
PFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIP
HLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSI
FGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYV
AQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVP
SRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFG
KRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDG
RTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQF
GGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVP
EPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASK
Ligand information
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]
PDB5d4d The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		R1031 M1035
Binding residue
(residue number reindexed from 1)		R1004 M1008
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:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
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:5d4d, PDBe:5d4d, PDBj:5d4d
PDBsum5d4d
PubMed27383794
UniProtQ8RQE9|RPOB_THET8 DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

[Back to BioLiP]