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Crystal structure of ATG13 lir-fused human LC3A_2-121

Analyse Crystal structure of ATG13 lir-fused human LC3A_2-121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WAN
Type: protein
Length: 254 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Autophagy-related protein 13, microtubule-associated proteins 1A/1B light chain 3A
UniProt: O75143, Q9H492
Pockets: 4 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Autophagy-related protein 13, microtubule-associated proteins 1A/1B light chain 3A	protein	126	32% helix, 19% strand	O75143, Q9H492
B	Autophagy-related protein 13, microtubule-associated proteins 1A/1B light chain 3A	protein	128	29% helix, 21% strand	O75143, Q9H492

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	154	0.46	0.76	20	empty
2	102	0.35	0.74	18	empty
3	70	0.35	0.76	20	empty
4	60	0.26	0.72	16	empty

Interfaces

1 interface between chains.

A–B · 704 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3WAN · Crystal structure of Atg13 LIR-fused human LC3A_2-121 · the same entry in another collection · chain A against A, TM-score 1.00
Q9H492 · AlphaFold monomer V2.0 prediction for microtubule-associated proteins 1A/1B light chain… · a predicted model of the same protein · chain A against A, TM-score 0.89
O75143 · AlphaFold monomer V2.0 prediction for autophagy-related protein 13 (O75143) · a predicted model of the same protein · chain B against A, TM-score 0.33

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 O75143
Every structure of UniProt Q9H492
Elsewhere: RCSB PDB 3WAN · PDBe 3WAN · UniProt O75143 · UniProt Q9H492

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