Research workbench
X-ray crystal structure of VAPB12 antitoxin from mycobacterium tuberculosis in space group P41.
Analyse X-ray crystal structure of VAPB12 antitoxin from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E4J
- Type
- protein
- Length
- 176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitoxin
- UniProt
- A0A045KH53
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Antitoxin | protein | 44 | 61% helix, 23% strand | A0A045KH53 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.26 | 0.72 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1576 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1535 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 190 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 160 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7E4J · X-ray crystal structure of VapB12 antitoxin from mycobacterium tuberculosis in space… · 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 A0A045KH53
- Elsewhere: RCSB PDB 7E4J · PDBe 7E4J · UniProt A0A045KH53
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