Research workbench

Vibrio cholerae ParD2 Antitoxin

Analyse Vibrio cholerae ParD2 Antitoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B22
Type: protein
Length: 392 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.08
Source: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Molecule: Antitoxin ParD
UniProt: P58093
Pockets: 7 · best druggability 0.50

Structure

x-ray diffraction · resolution 3.08 · 1 distinct chain · 65% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Antitoxin ParD	protein	49	65% helix, 6% strand	P58093

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.50	0.82	24	empty
2	88	0.44	0.80	17	empty
3	89	0.44	0.80	17	empty
4	90	0.44	0.79	21	empty
5	56	0.42	0.82	19	empty

Interfaces

13 interfaces between chains.

C–D · 1482 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 1480 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1465 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1410 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 476 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

7B22 · Vibrio cholerae PARD2 antitoxin · the same entry in another collection · chain H against H, TM-score 1.00
P58093 · AlphaFold monomer V2.0 prediction for antitoxin pard (P58093) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P58093
Elsewhere: RCSB PDB 7B22 · PDBe 7B22 · UniProt P58093

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