Research workbench

Crystal structure of the R59P-SNAP25 containing snare complex

Analyse Crystal structure of the R59P-SNAP25 containing snare complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WVW
Type: protein
Length: 529 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vesicle-associated membrane protein 2; Syntaxin-1A; Synaptosomal-associated protein 25
UniProt: P63045, P32851, P60881
Ligands: CA
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 7 distinct chains · 96% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vesicle-associated membrane protein 2	protein	62	95% helix, 0% strand	P63045
B, F	Syntaxin-1A	protein	66	97% helix, 0% strand	P32851
C	Synaptosomal-associated protein 25	protein	73	96% helix, 0% strand	P60881
D	Synaptosomal-associated protein 25	protein	63	97% helix, 0% strand	P60881
E	Vesicle-associated membrane protein 2	protein	63	95% helix, 0% strand	P63045
G	Synaptosomal-associated protein 25	protein	74	96% helix, 0% strand	P60881
H	Synaptosomal-associated protein 25	protein	62	97% helix, 0% strand	P60881

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains B, C, D, E, F
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains C, D, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	435	0.61	0.76	51	CA
2	440	0.59	0.75	50	empty
3	128	0.41	0.75	25	empty

Interfaces

19 interfaces between chains.

B–C · 1667 Å² buried · 15 hydrogen bonds · protein-protein
F–G · 1626 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1566 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1561 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1542 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6WVW · Crystal structure of the R59P-SNAP25 containing SNARE complex · the same entry in another collection · chain H against H, TM-score 1.00
P32851 · AlphaFold monomer V2.0 prediction for syntaxin-1A (P32851) · a predicted model of the same protein · chain B against A, TM-score 0.80
P63045 · AlphaFold monomer V2.0 prediction for vesicle-associated membrane protein 2 (P63045) · a predicted model of the same protein · chain E against A, TM-score 0.80

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 P63045
Every structure of UniProt P32851
Every structure of UniProt P60881
Elsewhere: RCSB PDB 6WVW · PDBe 6WVW · UniProt P63045 · UniProt P32851 · UniProt P60881

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