MolNFT v1 · #49472 · protein

Crystal structure of S.CEREVISIAE VPS4 in the presence of ADP

2QPA · Vacuolar protein sorting-associated protein 4: “Crystal structure of S.CEREVISIAE VPS4 in the presence of ADP”. X-ray diffraction, 2 ligands (ADP, PO4), 12 pockets (best druggability 0.75). MolNFT v1 #49472 on GenesisL1: 3D…

PDB: 2QPA
Type: protein
Length: 904 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 4
UniProt: P52917
Ligands: ADP, PO4
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein 4	protein	305	42% helix, 11% strand	P52917
B	Vacuolar protein sorting-associated protein 4	protein	303	40% helix, 13% strand	P52917
C	Vacuolar protein sorting-associated protein 4	protein	296	40% helix, 11% strand	P52917

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
PO4 · Phosphate ion · ion · 2 copies · chains B, C

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

Pockets

12 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	387	0.75	0.85	45	empty
2	196	0.73	0.89	40	empty
3	121	0.47	0.78	16	empty
4	100	0.46	0.80	19	empty
5	80	0.43	0.80	17	empty

Interfaces

2 interfaces between chains.

A–B · 730 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 697 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2QPA · Crystal Structure of S.cerevisiae Vps4 in the presence of ADP · the same entry in another collection · chain A against A, TM-score 1.00
P52917 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 4… · a predicted model of the same protein · chain A against A, TM-score 0.93

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
Elsewhere: RCSB PDB 2QPA · PDBe 2QPA · UniProt P52917

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