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Crystal structure of the human beta-2-syntrophin PDZ domain

Analyse Crystal structure of the human beta-2-syntrophin PDZ domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VRF
Type: protein
Length: 380 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: HOMO SAPIENS
Molecule: Beta-2-syntrophin
UniProt: Q13425
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · resolution 2 · 1 distinct chain · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-2-syntrophin	protein	95	18% helix, 41% strand	Q13425

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 3 copies · chains A, C

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

Pockets

5 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	228	0.57	0.79	39	empty
2	137	0.55	0.82	30	empty
3	138	0.52	0.81	36	empty
4	103	0.44	0.78	15	empty
5	57	0.34	0.78	20	empty

Interfaces

3 interfaces between chains.

A–B · 1199 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1178 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 424 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2VRF · Crystal structure of the human beta-2-syntrophin PDZ domain · the same entry in another collection · chain A against A, TM-score 1.00
Q13425 · AlphaFold monomer V2.0 prediction for beta-2-syntrophin (Q13425) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q13425
Elsewhere: RCSB PDB 2VRF · PDBe 2VRF · UniProt Q13425

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