MolNFT v1 · #66560 · protein

Crystal structure of the human VPS25-VPS20 subcomplex

3HTU · Vacuolar protein-sorting-associated protein 25: “Crystal structure of the human VPS25-VPS20 subcomplex”. X-ray diffraction, 4 pockets (best druggability 0.47). MolNFT v1 #66560 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3HTU
Type: protein
Length: 439 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein-sorting-associated protein 25; Vacuolar protein-sorting-associated…
UniProt: Q9BRG1, Q96FZ7
Pockets: 4 · best druggability 0.47

Structure

x-ray diffraction · 4 distinct chains · 65% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Vacuolar protein-sorting-associated protein 25	protein	75	43% helix, 13% strand	Q9BRG1
B	Vacuolar protein-sorting-associated protein 20	protein	35	83% helix, 0% strand	Q96FZ7
D, H	Vacuolar protein-sorting-associated protein 20	protein	36	78% helix, 0% strand	Q96FZ7
F	Vacuolar protein-sorting-associated protein 20	protein	32	81% helix, 0% strand	Q96FZ7

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	196	0.47	0.75	28	empty
2	84	0.35	0.75	26	empty
3	64	0.34	0.77	22	empty
4	61	0.34	0.77	19	empty

Interfaces

10 interfaces between chains.

B–D · 818 Å² buried · 5 hydrogen bonds · protein-protein
G–H · 816 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 811 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 792 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 779 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

3HTU · Crystal structure of the human VPS25-VPS20 subcomplex · the same entry in another collection · chain H against H, TM-score 1.00
Q9BRG1 · AlphaFold monomer V2.0 prediction for vacuolar protein-sorting- associated protein 25… · a predicted model of the same protein · chain A against A, TM-score 0.91
Q96FZ7 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 6 (Q96FZ7) · a predicted model of the same protein · chain D against A, TM-score 0.81

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 Q9BRG1
Every structure of UniProt Q96FZ7
Elsewhere: RCSB PDB 3HTU · PDBe 3HTU · UniProt Q9BRG1 · UniProt Q96FZ7

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