BioLiP

Structure of PDB 5d4d Chain P Binding Site BS02

Receptor Information

>5d4d Chain P (length=316) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLI
REVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIA
REGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF
EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ
LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDS
FYGDFIPDEHLPSPVDAATQSLLSEELEKREAMVLKLERIRQIENKALRK
LKYHESRTRKLRDFLD

Ligand information

>5d4d Chain S (length=21) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

tataatgggagcacggatgca

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5d4d The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.
Resolution	3.0 Å
Binding residue (original residue number in PDB)	D79 V81 R82 L85 G89 L93 N191 R193 L194 S197 F209 F227 F233 K234 S236 T237 Y238 T240 W241
Binding residue (residue number reindexed from 1)	D2 V4 R5 L8 G12 L16 N114 R116 L117 S120 F132 F150 F156 K157 S159 T160 Y161 T163 W164

Enzymatic activity

Enzyme Commision number

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003700	DNA-binding transcription factor activity
GO:0016987	sigma factor activity
GO:0046872	metal ion binding

	Biological Process
GO:0006352	DNA-templated transcription initiation
GO:0006355	regulation of DNA-templated transcription
GO:0010468	regulation of gene expression
GO:2000142	regulation of DNA-templated transcription initiation

	Cellular Component
GO:0005737	cytoplasm

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PDB	RCSB:5d4d, PDBe:5d4d, PDBj:5d4d
PDBsum	5d4d
PubMed	27383794
UniProt	Q5SKW1