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Truncated snare complex

Analyse Truncated snare complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RK2
Type: protein
Length: 464 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: P63027, P32851, P60880
Ligands: CA
Pockets: 9 · best druggability 0.56

Structure

x-ray diffraction · 5 distinct chains · 95% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vesicle-associated membrane protein 2	protein	30	93% helix, 0% strand	P63027
B, F	Syntaxin-1A	protein	59	97% helix, 0% strand	P32851
C, G	Synaptosomal-associated protein 25	protein	77	95% helix, 0% strand	P60880
D, H	Synaptosomal-associated protein 25	protein	65	94% helix, 0% strand	P60880
E	Vesicle-associated membrane protein 2	protein	32	94% helix, 0% strand	P63027

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains B, C, G

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

Pockets

9 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	220	0.56	0.79	27	empty
2	155	0.52	0.80	20	CA
3	190	0.47	0.75	22	empty
4	95	0.40	0.76	18	empty
5	85	0.38	0.76	18	empty

Interfaces

17 interfaces between chains.

G–H · 1629 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1620 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1545 Å² buried · 10 hydrogen bonds · protein-protein
F–G · 1536 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 948 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

3RK2 · Truncated SNARE complex · the same entry in another collection · chain H against H, TM-score 1.00
P60880 · AlphaFold monomer V2.0 prediction for synaptosomal-associated protein 25 (P60880) · a predicted model of the same protein · chain D against A, TM-score 0.92
P63027 · AlphaFold monomer V2.0 prediction for vesicle-associated membrane protein 2 (P63027) · a predicted model of the same protein · chain A against A, TM-score 0.86

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 P63027
Every structure of UniProt P32851
Every structure of UniProt P60880
Elsewhere: RCSB PDB 3RK2 · PDBe 3RK2 · UniProt P63027 · UniProt P32851 · UniProt P60880

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