MolNFT v1 · #134329 · protein

Synaptotagmin 1 C2B domain, cadmium-bound

5T0S · Synaptotagmin-1: “Synaptotagmin 1 C2B domain, cadmium-bound”. X-ray diffraction, 2 ligands (CD, NA), 1 pocket (best druggability 0.33). MolNFT v1 #134329 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5T0S
Type: protein
Length: 151 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Synaptotagmin-1
UniProt: P46096
Ligands: CD, NA
Pockets: 1 · best druggability 0.33

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Synaptotagmin-1	protein	151	15% helix, 45% strand	P46096

Ligands and binding sites

CD · Cadmium ion · metal · chains A
NA · Sodium ion · metal · chains A

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	59	0.33	0.77	12	NA

Compared structures

5T0S · Synaptotagmin 1 C2B domain, cadmium-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 0.96

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 5T0S · PDBe 5T0S · UniProt P46096

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