Research workbench
Asymmetry in the active site of mycobacterium tuberculosis ahpe upon exposure to mycothiol
Analyse Asymmetry in the active site of mycobacterium tuberculosis ahpe upon exposure… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ID2
- Type
- protein
- Length
- 623 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative peroxiredoxin RV2238C
- EC
- 1.11.1.15
- UniProt
- P9WIE3
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative peroxiredoxin RV2238C (EC 1.11.1.15) | protein | 154 | 28% helix, 27% strand | P9WIE3 |
| B, C | Putative peroxiredoxin RV2238C (EC 1.11.1.15) | protein | 157 | 27% helix, 26% strand | P9WIE3 |
| D | Putative peroxiredoxin RV2238C (EC 1.11.1.15) | protein | 155 | 28% helix, 25% strand | P9WIE3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.72 | 0.76 | 99 | GOL |
| 2 | 69 | 0.44 | 0.82 | 17 | empty |
| 3 | 55 | 0.33 | 0.77 | 13 | empty |
| 4 | 69 | 0.30 | 0.73 | 18 | empty |
| 5 | 65 | 0.29 | 0.73 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 735 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 732 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 365 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 162 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5ID2 · Asymmetry in the active site of Mycobacterium tuberculosis AhpE upon exposure to Mycothiol · the same entry in another collection · chain D against D, TM-score 1.00
- P9WIE3 · AlphaFold monomer V2.0 prediction for alkyl hydroperoxide reductase E (P9WIE3) · 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 P9WIE3
- Elsewhere: RCSB PDB 5ID2 · PDBe 5ID2 · UniProt P9WIE3
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