MolNFT v1 · #119610 · protein

The complex structure of syntenin-1 PDZ domain with C-terminal extension

5G1E: “The complex structure of syntenin-1 PDZ domain with C-terminal extension”. X-ray diffraction, 4 pockets (best druggability 0.53). MolNFT v1 #119610 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5G1E
Type: protein
Length: 333 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Syntenin-1
UniProt: Q9JI92
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Syntenin-1	protein	169	20% helix, 38% strand	Q9JI92
B	Syntenin-1	protein	164	21% helix, 35% strand	Q9JI92

Pockets

4 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	220	0.53	0.77	25	empty
2	87	0.47	0.81	20	empty
3	62	0.35	0.77	13	empty
4	67	0.34	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 1156 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5G1E · The complex structure of syntenin-1 PDZ domain with c-terminal extension · the same entry in another collection · chain A against A, TM-score 1.00
Q9JI92 · AlphaFold monomer V2.0 prediction for syntenin-1 (Q9JI92) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q9JI92
Elsewhere: RCSB PDB 5G1E · PDBe 5G1E · UniProt Q9JI92

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