MolNFT v1 · #29254 · protein

Crystal structure of mouse VPS29 complexed with MN2+

1Z2W · Vacuolar protein sorting 29: “Crystal structure of mouse VPS29 complexed with MN2+”. X-ray diffraction, 1 ligand (MN), 1 pocket (best druggability 0.47). MolNFT v1 #29254 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1Z2W
Type: protein
Length: 364 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting 29
UniProt: Q9QZ88
Ligands: MN
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Vacuolar protein sorting 29	protein	182	14% helix, 38% strand	Q9QZ88

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · 5 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.47	0.84	15	empty

Interfaces

1 interface between chains.

A–B · 1254 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

1Z2W · Crystal structure of mouse Vps29 complexed with Mn2+ · the same entry in another collection · chain A against A, TM-score 1.00
Q9QZ88 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 29… · a predicted model of the same protein · chain A against A, TM-score 0.91

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 Q9QZ88
Elsewhere: RCSB PDB 1Z2W · PDBe 1Z2W · UniProt Q9QZ88

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