MolNFT v1 · #128428 · protein

Structure of human ATG5-ATG16L1(ATG5BD) complex (C2)

5NPW · Autophagy protein 5: “Structure of human ATG5-ATG16L1(ATG5BD) complex (C2)”. X-ray diffraction, 9 pockets (best druggability 0.83). MolNFT v1 #128428 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NPW
Type: protein
Length: 1,221 residues
Chains: 8
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: 9 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Autophagy protein 5	protein	266	37% helix, 18% strand	Q9H1Y0
B	Autophagy-related protein 16-1	protein	40	88% helix, 0% strand	Q676U5
C	Autophagy protein 5	protein	268	35% helix, 19% strand	Q9H1Y0
D	Autophagy-related protein 16-1	protein	40	85% helix, 0% strand	Q676U5
E	Autophagy protein 5	protein	266	36% helix, 19% strand	Q9H1Y0
F	Autophagy-related protein 16-1	protein	39	87% helix, 0% strand	Q676U5
G	Autophagy protein 5	protein	261	36% helix, 18% strand	Q9H1Y0
H	Autophagy-related protein 16-1	protein	41	88% helix, 0% strand	Q676U5

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1118	0.83	0.84	99	empty
2	1183	0.80	0.81	109	empty
3	526	0.76	0.83	53	empty
4	94	0.54	0.84	22	empty
5	74	0.51	0.85	21	empty

Interfaces

13 interfaces between chains.

C–D · 1316 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 1289 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1177 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1169 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 753 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5NPW · Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) · the same entry in another collection · chain H against H, TM-score 1.00
Q9H1Y0 · AlphaFold monomer V2.0 prediction for autophagy protein 5 (Q9H1Y0) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 5NPW · PDBe 5NPW · UniProt Q9H1Y0 · UniProt Q676U5

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