MolNFT v1 · #139330 · protein

Crystal structure of wild type VPS29 complexed with ZN+2 from entamoeba histolytica

5XCH · Vacuolar protein sorting-associated protein 29: “Crystal structure of wild type VPS29 complexed with ZN+2 from entamoeba histolytica”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.72). MolNFT v1 #139330 on…

PDB: 5XCH
Type: protein
Length: 360 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vacuolar protein sorting-associated protein 29
UniProt: Q9BI08
Ligands: ZN
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Vacuolar protein sorting-associated protein 29	protein	180	13% helix, 34% strand	Q9BI08

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.72	0.96	13	empty
2	78	0.68	0.92	15	empty
3	281	0.54	0.75	36	empty
4	96	0.37	0.74	10	empty

Interfaces

1 interface between chains.

A–B · 447 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5XCH · Crystal structure of Wild type Vps29 complexed with Zn+2 from Entamoeba histolytica · 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 Q9BI08
Elsewhere: RCSB PDB 5XCH · PDBe 5XCH · UniProt Q9BI08

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