Research workbench
Crystal structure of peroxiredoxin (ahpc) from amphibacillus xylanus
Analyse Crystal structure of peroxiredoxin (ahpc) from amphibacillus xylanus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WE0
- Type
- protein
- Length
- 1,660 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyl hydroperoxide reductase C
- EC
- 1.11.1.-
- UniProt
- O87200
- Ligands
- NH4
- Pockets
- 20 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Alkyl hydroperoxide reductase C (EC 1.11.1.-) | protein | 166 | 28% helix, 27% strand | O87200 |
Ligands and binding sites
- NH4 · Ammonium ion · ion · 2 copies · chains F, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.60 | 0.89 | 15 | empty |
| 2 | 72 | 0.60 | 0.89 | 16 | empty |
| 3 | 64 | 0.57 | 0.88 | 14 | empty |
| 4 | 73 | 0.55 | 0.86 | 14 | empty |
| 5 | 198 | 0.54 | 0.79 | 41 | empty |
Interfaces
10 interfaces between chains.
- I–J · 1152 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1151 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1143 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1138 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1127 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1WE0 · Crystal structure of peroxiredoxin (AhpC) from Amphibacillus xylanus · 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 O87200
- Elsewhere: RCSB PDB 1WE0 · PDBe 1WE0 · UniProt O87200
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