MolNFT v1 · #87317 · protein

Human VPS33A

4BX8 · Vacuolar protein sorting-associated protein 33A: “Human VPS33A”. X-ray diffraction, 1 ligand (CL), 18 pockets (best druggability 0.75). MolNFT v1 #87317 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4BX8
Type: protein
Length: 1,138 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 33A
UniProt: Q96AX1
Ligands: CL
Pockets: 18 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vacuolar protein sorting-associated protein 33A	protein	568	49% helix, 16% strand	Q96AX1
B	Vacuolar protein sorting-associated protein 33A	protein	570	48% helix, 16% strand	Q96AX1

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	767	0.75	0.80	79	empty
2	455	0.74	0.83	46	empty
3	618	0.68	0.77	76	empty
4	274	0.66	0.82	36	empty
5	212	0.62	0.82	25	empty

Interfaces

1 interface between chains.

A–B · 1289 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

4BX8 · Human Vps33A · the same entry in another collection · chain A against A, TM-score 1.00
Q96AX1 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 33A… · 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 Q96AX1
Elsewhere: RCSB PDB 4BX8 · PDBe 4BX8 · UniProt Q96AX1

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