MolNFT v1 · #145008 · protein

Crystal structure of an N-terminal fragment of VPS13.

6CBC · Vacuolar protein sorting-associated protein: “Crystal structure of an N-terminal fragment of VPS13.”. X-ray diffraction, 8 pockets (best druggability 0.75). MolNFT v1 #145008 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6CBC
Type: protein
Length: 518 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein
UniProt: G0S3B8
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein	protein	248	23% helix, 40% strand	G0S3B8
B	Vacuolar protein sorting-associated protein	protein	270	25% helix, 42% strand	G0S3B8

Pockets

8 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	847	0.75	0.78	70	empty
2	473	0.65	0.77	46	empty
3	71	0.47	0.83	25	empty
4	87	0.43	0.79	21	empty
5	89	0.35	0.74	22	empty

Interfaces

1 interface between chains.

A–B · 1483 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

6CBC · Crystal structure of an N-terminal fragment of Vps13. · the same entry in another collection · chain A against A, 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 G0S3B8
Elsewhere: RCSB PDB 6CBC · PDBe 6CBC · UniProt G0S3B8

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