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Crystal structure of RAD4-RAD23 bound to a mismatch DNA

Analyse Crystal structure of RAD4-RAD23 bound to a mismatch DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QSH
Type: protein + DNA
Length: 602 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein RAD4; UV excision repair protein RAD23; Top strand of the mismatch…
UniProt: P14736, P32628
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein RAD4	protein	502	39% helix, 19% strand	P14736
X	UV excision repair protein RAD23	protein	54	83% helix, 0% strand	P32628
W	Top strand of the mismatch DNA	dna	24	—	—
Y	Bottom strand of the mismatch DNA	dna	22	—	—

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	636	0.74	0.80	54	empty
2	461	0.70	0.81	47	empty
3	421	0.65	0.79	47	empty
4	211	0.50	0.76	20	empty
5	66	0.47	0.84	14	empty

Interfaces

4 interfaces between chains.

A–X · 1406 Å² buried · 7 hydrogen bonds · protein-protein
A–W · 1141 Å² buried · 20 hydrogen bonds · protein-nucleic
W–Y · 981 Å² buried · 85 hydrogen bonds · nucleic-nucleic
A–Y · 688 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

2QSH · Crystal structure of Rad4-Rad23 bound to a mismatch DNA · the same entry in another collection · chain W against W, TM-score 1.00
P14736 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD4 (P14736) · a predicted model of the same protein · chain A against A, TM-score 0.99
P32628 · AlphaFold monomer V2.0 prediction for UV excision repair protein RAD23 (P32628) · a predicted model of the same protein · chain X against A, TM-score 0.89

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P14736
Every structure of UniProt P32628
Elsewhere: RCSB PDB 2QSH · PDBe 2QSH · UniProt P14736 · UniProt P32628

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