Research workbench

Complex structure of vinn with L-aspartate

Analyse Complex structure of vinn with L-aspartate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WVN
Type: protein
Length: 742 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Non-ribosomal peptide synthetase
EC: 6.2.1.-
UniProt: Q76KY2
Ligands: ASP
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Non-ribosomal peptide synthetase (EC 6.2.1.-)	protein	387	37% helix, 22% strand	Q76KY2
B	Non-ribosomal peptide synthetase (EC 6.2.1.-)	protein	355	39% helix, 22% strand	Q76KY2

Ligands and binding sites

ASP · Aspartic acid · ligand · 2 copies · chains A, B

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

Pockets

3 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	718	0.69	0.77	62	empty
2	266	0.57	0.78	42	ASP
3	117	0.44	0.78	22	ASP

Interfaces

1 interface between chains.

A–B · 487 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3WVN · Complex structure of VinN with L-aspartate · 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 Q76KY2
Elsewhere: RCSB PDB 3WVN · PDBe 3WVN · UniProt Q76KY2

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