MolNFT v1 · #103033 · protein

Extended-synaptotagmin 2, smp - C2A - C2B domains

4P42 · Extended synaptotagmin-2: “Extended-synaptotagmin 2, smp - C2A - C2B domains”. X-ray diffraction, 2 ligands (EGC, PEE), 8 pockets (best druggability 0.91). MolNFT v1 #103033 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4P42
Type: protein
Length: 886 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Extended synaptotagmin-2
UniProt: A0FGR8
Ligands: EGC, PEE
Pockets: 8 · best druggability 0.91

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Extended synaptotagmin-2	protein	455	17% helix, 47% strand	A0FGR8
B	Extended synaptotagmin-2	protein	431	17% helix, 48% strand	A0FGR8

Ligands and binding sites

EGC · 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-tetramethyl-butyl)-phenoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 2 copies · chains A, B
PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1041	0.91	0.92	114	EGC, PEE
2	1155	0.76	0.79	110	empty
3	142	0.58	0.83	20	empty
4	157	0.43	0.74	26	empty
5	96	0.39	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 3130 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

4P42 · Extended-Synaptotagmin 2, SMP - C2A - C2B Domains · the same entry in another collection · chain A against A, TM-score 1.00
A0FGR8 · AlphaFold monomer V2.0 prediction for extended synaptotagmin-2 (A0FGR8) · a predicted model of the same protein · chain B against A, TM-score 0.95

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 A0FGR8
Elsewhere: RCSB PDB 4P42 · PDBe 4P42 · UniProt A0FGR8

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