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Crystal structure of RAD50 bound to ADP

Analyse Crystal structure of RAD50 bound to ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AUY
Type: protein
Length: 723 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA double-strand break repair RAD50 ATPase
UniProt: Q58718
Ligands: ADP, MG
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA double-strand break repair RAD50 ATPase	protein	366	48% helix, 26% strand	Q58718
B	DNA double-strand break repair RAD50 ATPase	protein	357	47% helix, 27% strand	Q58718

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

7 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	504	0.77	0.84	53	empty
2	54	0.61	0.92	15	empty
3	144	0.55	0.81	26	empty
4	193	0.50	0.76	38	empty
5	96	0.47	0.81	28	ADP, MG

Interfaces

1 interface between chains.

A–B · 1645 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3AUY · Crystal structure of Rad50 bound to ADP · the same entry in another collection · chain B against B, TM-score 1.00
Q58718 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair RAD50 ATPase (Q58718) · a predicted model of the same protein · chain A against A, TM-score 0.82

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 Q58718
Elsewhere: RCSB PDB 3AUY · PDBe 3AUY · UniProt Q58718

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