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The catalytic core of RAD2 (complex I)

Analyse The catalytic core of RAD2 (complex I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q0R
Type: protein + DNA
Length: 574 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein RAD2; DNA (5'-D(*CP*TP*GP*AP*GP*TP*CP*AP*GP*AP*GP*CP*AP*AP*A)- 3')
EC: 3.1.-.-
UniProt: P07276
Pockets: 7 · best druggability 0.43

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein RAD2 (EC 3.1.-.-)	protein	293	51% helix, 11% strand	P07276
B	DNA repair protein RAD2 (EC 3.1.-.-)	protein	277	50% helix, 11% strand	P07276
D	DNA (5'-D(CPTPGPAPGPTPCPAPGPAPGPCPAPAP*A)- 3')	dna	4	—	—

Pockets

7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.43	0.77	23	empty
2	150	0.43	0.75	33	empty
3	111	0.42	0.77	22	empty
4	119	0.38	0.73	19	empty
5	108	0.34	0.72	13	empty

Interfaces

2 interfaces between chains.

A–B · 554 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 172 Å² buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

4Q0R · The catalytic core of Rad2 (complex I) · the same entry in another collection · chain A against A, TM-score 1.00
P07276 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD2 (P07276) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P07276
Elsewhere: RCSB PDB 4Q0R · PDBe 4Q0R · UniProt P07276

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