MolNFT v1 · #58497 · protein

Structure of the yeast plasma membrane snare complex

3B5N · Synaptobrevin homolog 1: “Structure of the yeast plasma membrane snare complex”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #58497 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3B5N
Type: protein
Length: 771 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Synaptobrevin homolog 1; Protein SSO1; Protein transport protein SEC9
UniProt: P31109, P32867, P40357
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 11 distinct chains · 96% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Synaptobrevin homolog 1	protein	61	97% helix, 0% strand	P31109
B	Protein SSO1	protein	69	97% helix, 0% strand	P32867
C	Protein transport protein SEC9	protein	70	97% helix, 0% strand	P40357
D	Protein transport protein SEC9	protein	64	94% helix, 0% strand	P40357
E, I	Synaptobrevin homolog 1	protein	58	95% helix, 0% strand	P31109
F	Protein SSO1	protein	68	97% helix, 0% strand	P32867
G	Protein transport protein SEC9	protein	69	97% helix, 0% strand	P40357
H	Protein transport protein SEC9	protein	63	95% helix, 0% strand	P40357
J	Protein SSO1	protein	64	95% helix, 0% strand	P32867
K	Protein transport protein SEC9	protein	65	95% helix, 0% strand	P40357
L	Protein transport protein SEC9	protein	62	94% helix, 0% strand	P40357

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	807	0.68	0.75	66	empty
2	509	0.64	0.76	47	empty
3	228	0.46	0.73	25	empty

Interfaces

24 interfaces between chains.

B–C · 1746 Å² buried · 19 hydrogen bonds · protein-protein
F–G · 1709 Å² buried · 19 hydrogen bonds · protein-protein
J–K · 1598 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 1582 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1541 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

3B5N · Structure of the yeast plasma membrane SNARE complex · the same entry in another collection · chain L against L, 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 P31109
Every structure of UniProt P32867
Every structure of UniProt P40357
Elsewhere: RCSB PDB 3B5N · PDBe 3B5N · UniProt P31109 · UniProt P32867 · UniProt P40357

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