Research workbench

Crystal structure of human ATG5-ATG16N69

Analyse Crystal structure of human ATG5-ATG16N69 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4TQ0
Type: protein
Length: 852 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Autophagy protein 5; Autophagy-related protein 16-1
UniProt: Q9H1Y0, Q676U5
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Autophagy protein 5	protein	244	39% helix, 21% strand	Q9H1Y0
B, F	Autophagy-related protein 16-1	protein	40	90% helix, 0% strand	Q676U5
C	Autophagy protein 5	protein	248	39% helix, 21% strand	Q9H1Y0
D	Autophagy-related protein 16-1	protein	37	92% helix, 0% strand	Q676U5
E	Autophagy protein 5	protein	243	35% helix, 20% strand	Q9H1Y0

Pockets

13 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	510	0.76	0.84	78	empty
2	53	0.73	0.99	18	empty
3	536	0.71	0.80	71	empty
4	292	0.59	0.78	34	empty
5	95	0.41	0.77	17	empty

Interfaces

6 interfaces between chains.

E–F · 1251 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 1195 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1189 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 862 Å² buried · 13 hydrogen bonds · protein-protein
C–E · 451 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4TQ0 · Crystal structure of human ATG5-ATG16N69 · the same entry in another collection · chain F against F, TM-score 1.00
Q9H1Y0 · AlphaFold monomer V2.0 prediction for autophagy protein 5 (Q9H1Y0) · a predicted model of the same protein · chain E against A, TM-score 0.98
Q676U5 · AlphaFold monomer V2.0 prediction for autophagy-related protein 16-1 (Q676U5) · a predicted model of the same protein · chain F against A, TM-score 0.72

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 Q9H1Y0
Every structure of UniProt Q676U5
Elsewhere: RCSB PDB 4TQ0 · PDBe 4TQ0 · UniProt Q9H1Y0 · UniProt Q676U5

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