MolNFT v1 · #35030 · protein

The crystal structure of saccharomyces cerevisiae ATG5- ATG16(1-46) complex

2DYM · Autophagy protein 5: “The crystal structure of saccharomyces cerevisiae ATG5- ATG16(1-46) complex”. X-ray diffraction, 10 pockets (best druggability 0.68). MolNFT v1 #35030 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2DYM
Type: protein
Length: 1,110 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Autophagy protein 5; Autophagy protein 16
UniProt: Q12380, Q03818
Pockets: 10 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Autophagy protein 5	protein	254	36% helix, 21% strand	Q12380
B, D, F, H	Autophagy protein 16	protein	24	83% helix, 0% strand	Q03818
C	Autophagy protein 5	protein	251	35% helix, 23% strand	Q12380
E	Autophagy protein 5	protein	247	37% helix, 23% strand	Q12380
G	Autophagy protein 5	protein	262	34% helix, 23% strand	Q12380

Pockets

10 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	51	0.68	0.97	15	empty
2	282	0.61	0.79	33	empty
3	300	0.60	0.78	25	empty
4	307	0.55	0.75	33	empty
5	213	0.48	0.75	24	empty

Interfaces

14 interfaces between chains.

A–B · 1322 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1322 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 1319 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1301 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 304 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2DYM · The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex · the same entry in another collection · chain H against H, TM-score 1.00
Q12380 · AlphaFold monomer V2.0 prediction for autophagy protein 5 (Q12380) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q12380
Every structure of UniProt Q03818
Elsewhere: RCSB PDB 2DYM · PDBe 2DYM · UniProt Q12380 · UniProt Q03818

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