MolNFT v1 · #186193 · protein

Vibrio cholera PARD2:PARE2 ANTITOXIN:TOXIN complex

7R5A: “Vibrio cholera PARD2:PARE2 ANTITOXIN:TOXIN complex”. X-ray diffraction, 3 pockets (best druggability 0.43). MolNFT v1 #186193 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7R5A
Type: protein
Length: 262 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin; Antitoxin pard
UniProt: Q9KMJ0, P58093
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 4 distinct chains · 59% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toxin	protein	94	43% helix, 29% strand	Q9KMJ0
B	Antitoxin pard	protein	73	73% helix, 3% strand	P58093
C	Antitoxin pard	protein	46	67% helix, 0% strand	P58093
D	Antitoxin pard	protein	49	61% helix, 0% strand	P58093

Pockets

3 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	142	0.43	0.75	21	empty
2	83	0.39	0.77	17	empty
3	63	0.37	0.78	14	empty

Interfaces

5 interfaces between chains.

A–B · 1380 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1214 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 501 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 247 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 41 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7R5A · Vibrio cholera ParD2:ParE2 antitoxin:toxin complex · the same entry in another collection · chain A against A, TM-score 1.00
P58093 · AlphaFold monomer V2.0 prediction for antitoxin pard (P58093) · a predicted model of the same protein · chain C against A, TM-score 0.86

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 Q9KMJ0
Every structure of UniProt P58093
Elsewhere: RCSB PDB 7R5A · PDBe 7R5A · UniProt Q9KMJ0 · UniProt P58093

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