MolNFT v1 · #174507 · protein

Crystal structure of the toxin-antitoxin with AMP-pnp

7BXO · Toxin-antitoxin system antidote mnt family: “Crystal structure of the toxin-antitoxin with AMP-pnp”. X-ray diffraction, 2 ligands (ANP, MG), 15 pockets (best druggability 0.83). MolNFT v1 #174507 on GenesisL1: 3D structure, binding…

PDB: 7BXO
Type: protein
Length: 1,034 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Toxin-antitoxin system antidote mnt family; Toxin-antitoxin system toxin hepn family
UniProt: Q8ECH7, Q8ECH6
Ligands: ANP, MG
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 68% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Toxin-antitoxin system antidote mnt family	protein	124	54% helix, 20% strand	Q8ECH7
B, C	Toxin-antitoxin system toxin hepn family	protein	132	75% helix, 0% strand	Q8ECH6
D	Toxin-antitoxin system toxin hepn family	protein	130	73% helix, 0% strand	Q8ECH6
E	Toxin-antitoxin system antidote mnt family	protein	125	50% helix, 18% strand	Q8ECH7
F	Toxin-antitoxin system toxin hepn family	protein	131	76% helix, 0% strand	Q8ECH6
G	Toxin-antitoxin system toxin hepn family	protein	131	75% helix, 0% strand	Q8ECH6
H	Toxin-antitoxin system toxin hepn family	protein	129	72% helix, 0% strand	Q8ECH6

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, D, H, E
MG · Magnesium ion · metal · 4 copies · chains A, E, H

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

Pockets

15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	650	0.83	0.88	61	ANP, MG
2	320	0.73	0.86	33	ANP, MG
3	238	0.66	0.84	34	empty
4	163	0.64	0.85	33	empty
5	328	0.63	0.79	46	empty

Interfaces

17 interfaces between chains.

D–H · 1092 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 961 Å² buried · 20 hydrogen bonds · protein-protein
F–G · 908 Å² buried · 20 hydrogen bonds · protein-protein
E–H · 780 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 721 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7BXO · Crystal structure of the toxin-antitoxin with AMP-PNP · the same entry in another collection · chain H against H, TM-score 1.00
Q8ECH7 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase mnta (Q8ECH7) · a predicted model of the same protein · chain A against A, TM-score 0.98
Q8ECH6 · AlphaFold monomer V2.0 prediction for mRNA nuclease hept (Q8ECH6) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q8ECH7
Every structure of UniProt Q8ECH6
Elsewhere: RCSB PDB 7BXO · PDBe 7BXO · UniProt Q8ECH7 · UniProt Q8ECH6

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