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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: 6AF4
Type: protein
Length: 834 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Higb toxin; Higa antitoxin
UniProt: A0A0H2UQ08, A0A0H2UQ20
Pockets: 8 · best druggability 0.57

Structure

x-ray diffraction · 7 distinct chains · 50% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Higb toxin	protein	119	45% helix, 24% strand	A0A0H2UQ08
B	Higa antitoxin	protein	90	63% helix, 13% strand	A0A0H2UQ20
C	Higb toxin	protein	118	42% helix, 25% strand	A0A0H2UQ08
D, H	Higa antitoxin	protein	92	62% helix, 13% strand	A0A0H2UQ20
E	Higb toxin	protein	117	39% helix, 26% strand	A0A0H2UQ08
F	Higa antitoxin	protein	91	60% helix, 13% strand	A0A0H2UQ20
G	Higb toxin	protein	115	44% helix, 24% strand	A0A0H2UQ08

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	342	0.57	0.76	40	empty
2	183	0.52	0.78	36	empty
3	143	0.52	0.80	26	empty
4	154	0.51	0.79	26	empty
5	263	0.49	0.74	30	empty

Interfaces

10 interfaces between chains.

C–D · 1655 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1604 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 1460 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 1429 Å² buried · 26 hydrogen bonds · protein-protein
D–F · 1326 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6AF4 · 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 6AF4 · PDBe 6AF4 · UniProt A0A0H2UQ08 · UniProt A0A0H2UQ20

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