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Structure of the atpgs-bound vat complex

Analyse Structure of the atpgs-bound vat complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5G4G
Type: protein
Length: 4,326 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vcp-like ATPase
UniProt: O05209
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 1 distinct chain · 37% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Vcp-like ATPase	protein	721	37% helix, 13% strand	O05209

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	981	0.89	0.91	158	empty
2	879	0.88	0.91	142	empty
3	882	0.88	0.90	130	empty
4	759	0.87	0.90	120	empty
5	906	0.87	0.88	125	empty

Interfaces

6 interfaces between chains.

C–E · 3021 Å² buried · 59 hydrogen bonds · protein-protein
E–F · 3019 Å² buried · 59 hydrogen bonds · protein-protein
B–C · 3018 Å² buried · 59 hydrogen bonds · protein-protein
A–D · 3017 Å² buried · 59 hydrogen bonds · protein-protein
D–F · 3014 Å² buried · 59 hydrogen bonds · protein-protein

Compared structures

O05209 · AlphaFold monomer V2.0 prediction for vcp-like ATPase (O05209) · a predicted model of the same protein · chain A against A, TM-score 0.75

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 O05209
Elsewhere: RCSB PDB 5G4G · PDBe 5G4G · UniProt O05209

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