MolNFT v1 · #48786 · protein

The RIM1ALPHA C2B domain

2Q3X · Regulating synaptic membrane exocytosis protein 1: “The RIM1ALPHA C2B domain”. X-ray diffraction, 3 ligands (NA, SO4, CL), 2 pockets (best druggability 0.70). MolNFT v1 #48786 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2Q3X
Type: protein
Length: 286 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regulating synaptic membrane exocytosis protein 1
UniProt: Q9JIR4
Ligands: NA, SO4, CL
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Regulating synaptic membrane exocytosis protein 1	protein	142	5% helix, 53% strand	Q9JIR4
B	Regulating synaptic membrane exocytosis protein 1	protein	144	5% helix, 53% strand	Q9JIR4

Ligands and binding sites

NA · Sodium ion · metal · chains B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
CL · Chloride ion · ion · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.70	0.96	23	empty
2	57	0.35	0.78	17	SO4

Interfaces

1 interface between chains.

A–B · 1019 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified (engineered).

Compared structures

2Q3X · The RIM1alpha C2B domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9JIR4 · AlphaFold monomer V2.0 prediction for regulating synaptic membrane exocytosis protein 1… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9JIR4
Elsewhere: RCSB PDB 2Q3X · PDBe 2Q3X · UniProt Q9JIR4

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