Research workbench

Truncated snare complex with complexin (P1)

Analyse Truncated snare complex with complexin (P1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RL0
Type: protein
Length: 2,187 residues
Chains: 40
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, O14810
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 21 distinct chains · 95% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, Q, U, Y	Vesicle-associated membrane protein 2	protein	35	94% helix, 0% strand	P63027
B	Syntaxin-1A	protein	59	97% helix, 0% strand	P32851
C, O, e	Synaptosomal-associated protein 25	protein	72	96% helix, 0% strand	P60880
D, T, f	Synaptosomal-associated protein 25	protein	62	97% helix, 0% strand	P60880
F, R	Syntaxin-1A	protein	61	97% helix, 0% strand	P32851
G	Synaptosomal-associated protein 25	protein	74	93% helix, 0% strand	P60880
H, b	Synaptosomal-associated protein 25	protein	61	97% helix, 0% strand	P60880
I, c	Vesicle-associated membrane protein 2	protein	34	94% helix, 0% strand	P63027
J, d	Syntaxin-1A	protein	59	97% helix, 0% strand	P32851
K	Synaptosomal-associated protein 25	protein	71	97% helix, 0% strand	P60880
L, P	Synaptosomal-associated protein 25	protein	64	97% helix, 0% strand	P60880
M	Vesicle-associated membrane protein 2	protein	36	94% helix, 0% strand	P63027
N	Syntaxin-1A	protein	57	96% helix, 0% strand	P32851
S, a	Synaptosomal-associated protein 25	protein	70	96% helix, 0% strand	P60880
V	Syntaxin-1A	protein	58	97% helix, 0% strand	P32851
W	Synaptosomal-associated protein 25	protein	70	97% helix, 0% strand	P60880
X	Synaptosomal-associated protein 25	protein	63	97% helix, 0% strand	P60880
Z	Syntaxin-1A	protein	58	97% helix, 0% strand	P32851
g, l	Complexin-1	protein	47	87% helix, 0% strand	O14810
h, k	Complexin-1	protein	46	89% helix, 0% strand	O14810
i, j, m, n	Complexin-1	protein	45	93% helix, 0% strand	O14810

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	667	0.81	0.86	60	empty
2	1034	0.81	0.82	85	empty
3	537	0.80	0.86	46	empty
4	576	0.79	0.85	68	empty
5	857	0.77	0.81	57	empty

Interfaces

118 interfaces between chains.

F–G · 1425 Å² buried · 8 hydrogen bonds · protein-protein
S–T · 1416 Å² buried · 15 hydrogen bonds · protein-protein
K–L · 1414 Å² buried · 10 hydrogen bonds · protein-protein
a–b · 1410 Å² buried · 14 hydrogen bonds · protein-protein
d–e · 1385 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

3RL0 · Truncated SNARE complex with complexin (P1) · the same entry in another collection · chain J against J, 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 P63027
Every structure of UniProt P32851
Every structure of UniProt P60880
Every structure of UniProt O14810
Elsewhere: RCSB PDB 3RL0 · PDBe 3RL0 · UniProt P63027 · UniProt P32851 · UniProt P60880 · UniProt O14810

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