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Crystal structure of the autophagic STX17/SNAP29/VAMP8 snare complex

Analyse Crystal structure of the autophagic STX17/SNAP29/VAMP8 snare complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BV6
Type: protein
Length: 1,583 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vesicle-associated membrane protein 8; Syntaxin-17; Synaptosomal-associated protein 29
UniProt: Q9BV40, P56962, O95721
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 14 distinct chains · 93% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I, M, U	Vesicle-associated membrane protein 8	protein	66	97% helix, 0% strand	Q9BV40
B, F	Syntaxin-17	protein	61	93% helix, 0% strand	P56962
C, W	Synaptosomal-associated protein 29	protein	72	96% helix, 0% strand	O95721
D, L	Synaptosomal-associated protein 29	protein	67	97% helix, 0% strand	O95721
E	Vesicle-associated membrane protein 8	protein	65	94% helix, 0% strand	Q9BV40
G, S	Synaptosomal-associated protein 29	protein	74	97% helix, 0% strand	O95721
H	Synaptosomal-associated protein 29	protein	68	96% helix, 0% strand	O95721
J	Syntaxin-17	protein	59	90% helix, 0% strand	P56962
K, O	Synaptosomal-associated protein 29	protein	73	93% helix, 0% strand	O95721
N, V	Syntaxin-17	protein	60	85% helix, 0% strand	P56962
P, X	Synaptosomal-associated protein 29	protein	65	95% helix, 0% strand	O95721
Q	Vesicle-associated membrane protein 8	protein	61	87% helix, 0% strand	Q9BV40
R	Syntaxin-17	protein	55	85% helix, 0% strand	P56962
T	Synaptosomal-associated protein 29	protein	67	91% helix, 0% strand	O95721

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	798	0.76	0.80	94	empty
2	768	0.74	0.79	86	empty
3	714	0.72	0.79	73	empty
4	767	0.71	0.78	75	empty
5	62	0.60	0.91	21	empty

Interfaces

68 interfaces between chains.

A–B · 1765 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1718 Å² buried · 13 hydrogen bonds · protein-protein
U–V · 1715 Å² buried · 20 hydrogen bonds · protein-protein
M–N · 1687 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1620 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

7BV6 · Crystal structure of the autophagic STX17/SNAP29/VAMP8 SNARE complex · the same entry in another collection · chain K against K, 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 Q9BV40
Every structure of UniProt P56962
Every structure of UniProt O95721
Elsewhere: RCSB PDB 7BV6 · PDBe 7BV6 · UniProt Q9BV40 · UniProt P56962 · UniProt O95721

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