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Crystal structure of RAD50 ABC-ATPase

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

PDB: 1F2U
Type: protein
Length: 584 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAD50 ABC-ATPase
UniProt: P58301
Ligands: ATP, MG
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAD50 ABC-ATPase	protein	149	26% helix, 40% strand	P58301
B	RAD50 ABC-ATPase	protein	145	43% helix, 29% strand	P58301
C	RAD50 ABC-ATPase	protein	148	26% helix, 39% strand	P58301
D	RAD50 ABC-ATPase	protein	142	43% helix, 27% strand	P58301

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B, D, C
MG · Magnesium ion · metal · 2 copies · chains A, B, D, C

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1076	0.82	0.83	128	MG, ATP
2	120	0.57	0.84	23	empty
3	130	0.46	0.77	17	empty
4	121	0.40	0.74	21	empty
5	52	0.38	0.81	19	empty

Interfaces

5 interfaces between chains.

C–D · 2240 Å² buried · 45 hydrogen bonds · protein-protein
A–B · 2220 Å² buried · 45 hydrogen bonds · protein-protein
A–D · 589 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 569 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 454 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1F2U · Crystal Structure of RAD50 ABC-ATPase · the same entry in another collection · chain D against D, TM-score 1.00
P58301 · AlphaFold monomer V2.0 prediction for DNA double-strand break repair RAD50 ATPase (P58301) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P58301
Elsewhere: RCSB PDB 1F2U · PDBe 1F2U · UniProt P58301

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