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Toxin-antitoxin module from streptococcus pneumoniae

Analyse Toxin-antitoxin module from streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AF3
Type: protein
Length: 819 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Higb toxin; Higa antitoxin
UniProt: A0A0H2UQ08, A0A0H2UQ20
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 8 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Higb toxin	protein	114	43% helix, 26% strand	A0A0H2UQ08
B	Higa antitoxin	protein	91	64% helix, 13% strand	A0A0H2UQ20
C	Higb toxin	protein	113	40% helix, 27% strand	A0A0H2UQ08
D	Higa antitoxin	protein	92	61% helix, 13% strand	A0A0H2UQ20
E	Higb toxin	protein	116	36% helix, 22% strand	A0A0H2UQ08
F	Higa antitoxin	protein	90	60% helix, 10% strand	A0A0H2UQ20
G	Higb toxin	protein	117	19% helix, 1% strand	A0A0H2UQ08
H	Higa antitoxin	protein	86	65% helix, 10% strand	A0A0H2UQ20

Pockets

10 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	1055	0.79	0.81	109	empty
2	114	0.77	0.96	28	empty
3	114	0.55	0.83	23	empty
4	85	0.46	0.81	20	empty
5	66	0.46	0.83	18	empty

Interfaces

11 interfaces between chains.

C–D · 1551 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1538 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 1419 Å² buried · 20 hydrogen bonds · protein-protein
B–H · 1329 Å² buried · 22 hydrogen bonds · protein-protein
D–F · 1254 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 modified (engineered).

Compared structures

6AF3 · Toxin-Antitoxin module from Streptococcus pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A0H2UQ08
Every structure of UniProt A0A0H2UQ20
Elsewhere: RCSB PDB 6AF3 · PDBe 6AF3 · UniProt A0A0H2UQ08 · UniProt A0A0H2UQ20

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