Research workbench

Crystal structure of vinj

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

PDB: 3WMR
Type: protein
Length: 888 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proline iminopeptidase
UniProt: Q76KY6
Ligands: P4G
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Proline iminopeptidase	protein	296	43% helix, 17% strand	Q76KY6

Ligands and binding sites

P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

6 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	212	0.68	0.85	31	empty
2	452	0.68	0.80	58	GOL
3	198	0.68	0.86	29	empty
4	172	0.65	0.85	29	empty
5	162	0.46	0.76	29	GOL

Interfaces

2 interfaces between chains.

A–B · 467 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 285 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3WMR · Crystal structure of VinJ · 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 Q76KY6
Elsewhere: RCSB PDB 3WMR · PDBe 3WMR · UniProt Q76KY6

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.