MolNFT v1 · #122026 · protein
Asymmetry in the active site of mycobacterium tuberculosis ahpe upon exposure to mycothiol
5ID2 · Putative peroxiredoxin RV2238C: “Asymmetry in the active site of mycobacterium tuberculosis ahpe upon exposure to mycothiol”. X-ray diffraction, 6 pockets (best druggability 0.72). MolNFT v1 #122026 on GenesisL1: 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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