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RAD51 (rada)

Analyse RAD51 (rada) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PZN
Type: protein
Length: 1,733 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair and recombination protein RAD51
UniProt: O74036
Ligands: SO4
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair and recombination protein RAD51	protein	300	41% helix, 20% strand	O74036
B, C, D, E, F	DNA repair and recombination protein RAD51	protein	239	36% helix, 25% strand	O74036
G	DNA repair and recombination protein RAD51	protein	238	33% helix, 26% strand	O74036

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, E, F, G
IMD · Imidazole · additive · 9 copies · chains A, B, G, C, E, F
GOL · Glycerol · additive · 9 copies · chains A, G, B, C, D, E, F
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B, D, E, G, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	631	0.73	0.80	73	SO4
2	738	0.73	0.79	68	SO4
3	754	0.72	0.78	76	SO4
4	683	0.72	0.79	77	SO4
5	535	0.69	0.79	52	SO4

Interfaces

9 interfaces between chains.

A–B · 1594 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1315 Å² buried · 16 hydrogen bonds · protein-protein
A–G · 1311 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 1292 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1278 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 modified (engineered).

Compared structures

1PZN · Rad51 (RadA) · the same entry in another collection · chain C against C, TM-score 1.00
O74036 · AlphaFold monomer V2.0 prediction for DNA repair and recombination protein rada (O74036) · a predicted model of the same protein · chain G against A, TM-score 0.96

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 O74036
Elsewhere: RCSB PDB 1PZN · PDBe 1PZN · UniProt O74036

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