MolNFT v1 · #137148 · protein

Synaptotagmin 1 C2A domain, lead-bound

5VFE · Synaptotagmin-1: “Synaptotagmin 1 C2A domain, lead-bound”. X-ray diffraction, 2 ligands (PB, SO4), 1 pocket (best druggability 0.44). MolNFT v1 #137148 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VFE
Type: protein
Length: 249 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Synaptotagmin-1
UniProt: P46096
Ligands: PB, SO4
Pockets: 1 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Synaptotagmin-1	protein	125	7% helix, 54% strand	P46096
B	Synaptotagmin-1	protein	124	7% helix, 52% strand	P46096

Ligands and binding sites

PB · Lead (II) ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	114	0.44	0.78	32	empty

Interfaces

1 interface between chains.

A–B · 382 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5VFE · Synaptotagmin 1 C2A domain, lead-bound · the same entry in another collection · chain A against A, TM-score 1.00
P46096 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P46096) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P46096
Elsewhere: RCSB PDB 5VFE · PDBe 5VFE · UniProt P46096

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