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Crystal structure of plant ATG12 complexed with the AIM12 of ATG3

Analyse Crystal structure of plant ATG12 complexed with the AIM12 of ATG3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EU4
Type: protein
Length: 1,198 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-like protein ATG12B; AIM12 from autophagy-related protein 3
UniProt: Q9LVK3, Q0WWQ1
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 11 distinct chains · 23% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-like protein ATG12B	protein	82	23% helix, 38% strand	Q9LVK3
B, D, F	Ubiquitin-like protein ATG12B	protein	85	22% helix, 40% strand	Q9LVK3
C, E	Ubiquitin-like protein ATG12B	protein	94	20% helix, 35% strand	Q9LVK3
G	Ubiquitin-like protein ATG12B	protein	81	23% helix, 36% strand	Q9LVK3
H, K	Ubiquitin-like protein ATG12B	protein	83	23% helix, 35% strand	Q9LVK3
I, J	Ubiquitin-like protein ATG12B	protein	84	23% helix, 37% strand	Q9LVK3
L	Ubiquitin-like protein ATG12B	protein	81	23% helix, 33% strand	Q9LVK3
M	Ubiquitin-like protein ATG12B	protein	81	23% helix, 36% strand	Q9LVK3
N	Ubiquitin-like protein ATG12B	protein	74	26% helix, 34% strand	Q9LVK3
O, R	AIM12 from autophagy-related protein 3	protein	5	0% helix, 20% strand	Q0WWQ1
P, Q	AIM12 from autophagy-related protein 3	protein	6	0% helix, 17% strand	Q0WWQ1

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	702	0.83	0.87	90	empty
2	505	0.81	0.87	68	empty
3	180	0.69	0.88	32	empty
4	230	0.67	0.84	27	empty
5	153	0.66	0.87	25	empty

Interfaces

55 interfaces between chains.

C–D · 3056 Å² buried · 62 hydrogen bonds · protein-protein
E–F · 2942 Å² buried · 55 hydrogen bonds · protein-protein
I–J · 2875 Å² buried · 57 hydrogen bonds · protein-protein
A–B · 2865 Å² buried · 58 hydrogen bonds · protein-protein
K–L · 2770 Å² buried · 50 hydrogen bonds · protein-protein

Compared structures

7EU4 · Crystal structure of plant ATG12 complexed with the AIM12 of ATG3 · the same entry in another collection · chain J against J, 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 Q9LVK3
Every structure of UniProt Q0WWQ1
Elsewhere: RCSB PDB 7EU4 · PDBe 7EU4 · UniProt Q9LVK3 · UniProt Q0WWQ1

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