MolNFT v1 · #123664 · protein

RAD52(1-212) K102A/K133A/E202A mutant

5JRB · DNA repair protein RAD52 homolog: “RAD52(1-212) K102A/K133A/E202A mutant”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #123664 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JRB
Type: protein
Length: 2,028 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein RAD52 homolog
UniProt: P43351
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	DNA repair protein RAD52 homolog	protein	184	41% helix, 30% strand	P43351
K	DNA repair protein RAD52 homolog	protein	188	39% helix, 29% strand	P43351

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	966	0.79	0.81	116	empty
2	416	0.70	0.81	55	empty
3	375	0.66	0.80	52	empty
4	414	0.66	0.79	50	empty
5	95	0.65	0.90	18	empty

Interfaces

22 interfaces between chains.

C–D · 2673 Å² buried · 41 hydrogen bonds · protein-protein
D–E · 2650 Å² buried · 43 hydrogen bonds · protein-protein
E–F · 2647 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2625 Å² buried · 39 hydrogen bonds · protein-protein
B–C · 2610 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

5JRB · Rad52(1-212) K102A/K133A/E202A mutant · the same entry in another collection · chain K against K, TM-score 1.00
P43351 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD52 homolog (P43351) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P43351
Elsewhere: RCSB PDB 5JRB · PDBe 5JRB · UniProt P43351

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