Research workbench

Molecular and structural characterization of the pezat chromosomal toxin-antitoxin system of the human pathogen streptococcus pneumoniae

Analyse Molecular and structural characterization of the pezat chromosomal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P5T
Type: protein
Length: 1,379 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fragment of peza helix-turn-helix motif; Putative transcriptional regulator peza; Pezt
UniProt: Q97QZ2, Q97QZ1
Pockets: 16 · best druggability 0.80

Structure

x-ray diffraction · 8 distinct chains · 58% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Fragment of peza helix-turn-helix motif	protein	33	58% helix, 0% strand	—
A	Putative transcriptional regulator peza	protein	92	78% helix, 0% strand	Q97QZ2
B	Pezt	protein	244	52% helix, 12% strand	Q97QZ1
C, G	Putative transcriptional regulator peza	protein	93	80% helix, 0% strand	Q97QZ2
D	Pezt	protein	247	53% helix, 12% strand	Q97QZ1
E	Putative transcriptional regulator peza	protein	95	74% helix, 0% strand	Q97QZ2
F	Pezt	protein	240	50% helix, 12% strand	Q97QZ1
H	Pezt	protein	242	54% helix, 13% strand	Q97QZ1

Pockets

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	941	0.80	0.82	93	empty
2	1127	0.80	0.81	100	empty
3	1070	0.75	0.78	98	empty
4	1119	0.74	0.77	81	empty
5	57	0.65	0.94	13	empty

Interfaces

10 interfaces between chains.

E–F · 1795 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1692 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 1638 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 1553 Å² buried · 26 hydrogen bonds · protein-protein
D–H · 1145 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

2P5T · Molecular and structural characterization of the PezAT chromosomal toxin-antitoxin system… · the same entry in another collection · chain H against H, TM-score 1.00
Q97QZ1 · AlphaFold monomer V2.0 prediction for toxin pezt (Q97QZ1) · a predicted model of the same protein · chain F against A, TM-score 0.98
Q97QZ2 · AlphaFold monomer V2.0 prediction for antitoxin peza (Q97QZ2) · a predicted model of the same protein · chain A 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 Q97QZ2
Every structure of UniProt Q97QZ1
Elsewhere: RCSB PDB 2P5T · PDBe 2P5T · UniProt Q97QZ2 · UniProt Q97QZ1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.