Research workbench

Crystal structure of lgg-1 complexed with a weel peptide

Analyse Crystal structure of lgg-1 complexed with a weel peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AZF
Type: protein
Length: 246 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein lgg-1; Peptide from autophagy-related protein 19
UniProt: Q09490, P35193
Ligands: CD, SO4
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein lgg-1	protein	119	32% helix, 20% strand	Q09490
C, D	Peptide from autophagy-related protein 19	protein	4	0% helix, 50% strand	P35193

Ligands and binding sites

CD · Cadmium ion · metal · 13 copies · chains A, B, D
SO4 · Sulfate ion · ion · chains 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	389	0.72	0.83	42	empty

Interfaces

3 interfaces between chains.

A–B · 580 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 499 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 483 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5AZF · Crystal structure of LGG-1 complexed with a WEEL peptide · the same entry in another collection · chain A against A, TM-score 1.00
P35193 · AlphaFold monomer V2.0 prediction for autophagy-related protein 19 (P35193) · a predicted model of the same protein · chain C against A, TM-score 0.95
Q09490 · AlphaFold monomer V2.0 prediction for protein lgg-1 (Q09490) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q09490
Every structure of UniProt P35193
Elsewhere: RCSB PDB 5AZF · PDBe 5AZF · UniProt Q09490 · UniProt P35193

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