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Crystallographic forms of the VPS75 tetramer

Analyse Crystallographic forms of the VPS75 tetramer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AGC
Type: protein
Length: 869 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 75
UniProt: P53853
Pockets: 10 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein 75	protein	217	51% helix, 14% strand	P53853
B	Vacuolar protein sorting-associated protein 75	protein	220	51% helix, 14% strand	P53853
C, D	Vacuolar protein sorting-associated protein 75	protein	216	51% helix, 14% strand	P53853

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	721	0.68	0.76	75	empty
2	552	0.64	0.76	35	empty
3	316	0.63	0.80	34	empty
4	204	0.56	0.79	23	empty
5	140	0.49	0.79	19	empty

Interfaces

5 interfaces between chains.

A–B · 655 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 352 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 321 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 59 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 37 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5AGC · Crystallographic forms of the Vps75 tetramer · the same entry in another collection · chain A against A, TM-score 1.00
P53853 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 75… · a predicted model of the same protein · chain A 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 P53853
Elsewhere: RCSB PDB 5AGC · PDBe 5AGC · UniProt P53853

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