Structure of PDB 7ml2 Chain 0

Receptor sequence
>7ml20 (length=754) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
MKFYIDDLPVLFPYPKIYPEQYNYMCDIKKTLDVGGNSILEMPSGTGKTV
SLLSLTIAYQMHYPEHRKIIYCSRTMSEIEKALVELENLMDYRTKELGYQ
EDFRGLGLTSRKNLCLHPEVSKERKGTVVDEKCRRMTNGQAKRKLEEDPE
ANVELCEYHENLYNIEVEDYLPKGVFSFEKLLKYCEEKTLCPYFIVRRMI
SLCNIIIYSYHYLLDPKIAERVSNEVSKDSIVIFDEAHNIDNVCIESLSL
DLTTDALRRATRGANALDERISEVRKVDSQKLQDEYEKLVQGLHSADILT
DQEEPFVETPVLPQDLLTEAIPGNIRRAEHFVSFLKRLIEYLKTRMKVLH
VISETPKSFLQHLKQLTFIERKPLRFCSERLSLLVRTLEVTEVEDFTALK
DIATFATLISTYEEGFLLIIEPYEIENAAVPNPIMRFTCLDASIAIKPVF
ERFSSVIITSGTISPLDMYPRMLNFKTVLQKSYAMTLAKKSFLPMIITKG
SDQVAISSRFEIRNDPSIVRNYGSMLVEFAKITPDGMVVFFPSYLYMESI
VSMWQTMGILDEVWKHKLILVETPDAQETSLALETYRKACSNGRGAILLS
VARGKVSEGIDFDHQYGRTVLMIGIPFQYTESRILKARLEFMRENYRIRE
NDFLSFDAMRHAAQCLGRVLRGKDDYGVMVLADRRFSRKRSQLPKWIAQG
LSDADLNLSTDMAISNTKQFLRTMAQPTDPKDQEGVSVWSYEDLIKHQNS
RKDQ
3D structure
PDB7ml2 Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Chain0
Resolution3.4 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 SF4 0 C115 L116 H117 C133 T137 C156 Y158 C191 Y193 F194 C115 L116 H117 C133 T137 C156 Y158 C191 Y193 F194
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0003684 damaged DNA binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0016853 isomerase activity
GO:0016887 ATP hydrolysis activity
GO:0043139 5'-3' DNA helicase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0000019 regulation of mitotic recombination
GO:0006139 nucleobase-containing compound metabolic process
GO:0006281 DNA repair
GO:0006289 nucleotide-excision repair
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006974 DNA damage response
GO:0032508 DNA duplex unwinding
GO:0045951 positive regulation of mitotic recombination
Cellular Component
GO:0000112 nucleotide-excision repair factor 3 complex
GO:0000439 transcription factor TFIIH core complex
GO:0005634 nucleus
GO:0005675 transcription factor TFIIH holo complex
GO:0005829 cytosol
GO:0032991 protein-containing complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7ml2, PDBe:7ml2, PDBj:7ml2
PDBsum7ml2
PubMed35051353
UniProtP06839|RAD3_YEAST General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 (Gene Name=RAD3)

[Back to BioLiP]