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Cryo-EM structure of the ATP-bound VPS4 mutant-E233Q complex with VTA1 (masked)

Analyse Cryo-EM structure of the ATP-bound VPS4 mutant-E233Q complex with VTA1 (masked) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XMK
Type: protein
Length: 2,298 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 4; Vacuolar protein sorting-associated…
UniProt: P52917, Q06263
Ligands: ATP
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 3 distinct chains · 55% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Vacuolar protein sorting-associated protein 4	protein	319	46% helix, 13% strand	P52917
G, I, K, M	Vacuolar protein sorting-associated protein VTA1	protein	54	81% helix, 0% strand	Q06263
H, J, L, N	Vacuolar protein sorting-associated protein VTA1	protein	42	83% helix, 0% strand	Q06263

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains B, C, D, E, F

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

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	792	0.87	0.90	104	ATP
2	827	0.86	0.89	108	ATP
3	686	0.85	0.88	107	empty
4	302	0.81	0.92	54	empty
5	942	0.81	0.83	101	ATP

Interfaces

29 interfaces between chains.

E–F · 2128 Å² buried · 24 hydrogen bonds · protein-protein
D–E · 2123 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2078 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 2073 Å² buried · 16 hydrogen bonds · protein-protein
A–F · 1372 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5XMK · Cryo-EM structure of the ATP-bound Vps4 mutant-E233Q complex with Vta1 (masked) · the same entry in another collection · chain N against N, TM-score 1.00

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 P52917
Every structure of UniProt Q06263
Elsewhere: RCSB PDB 5XMK · PDBe 5XMK · UniProt P52917 · UniProt Q06263

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