Research workbench
Crystal structure of the peroxiredoxin (AHPC2) from the hyperthermophilic bacteria aquifex aeolicus vf
Analyse Crystal structure of the peroxiredoxin (AHPC2) from the hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OVQ
- Type
- protein
- Length
- 2,624 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin
- EC
- 1.11.1.15
- UniProt
- O67024
- Ligands
- UNL
- Pockets
- 20 · best druggability 0.57
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, K | Peroxiredoxin (EC 1.11.1.15) | protein | 219 | 31% helix, 26% strand | O67024 |
| B | Peroxiredoxin (EC 1.11.1.15) | protein | 221 | 31% helix, 26% strand | O67024 |
| D, F, G, H, I | Peroxiredoxin (EC 1.11.1.15) | protein | 218 | 32% helix, 26% strand | O67024 |
| J | Peroxiredoxin (EC 1.11.1.15) | protein | 217 | 32% helix, 26% strand | O67024 |
| L | Peroxiredoxin (EC 1.11.1.15) | protein | 220 | 31% helix, 27% strand | O67024 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 11 copies · chains A, D, B, F, E, H, G, I, J, K, C, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.57 | 0.83 | 21 | empty |
| 2 | 111 | 0.55 | 0.84 | 21 | empty |
| 3 | 248 | 0.54 | 0.77 | 41 | empty |
| 4 | 290 | 0.54 | 0.75 | 39 | UNL |
| 5 | 284 | 0.54 | 0.76 | 43 | UNL |
Interfaces
12 interfaces between chains.
- K–L · 2846 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2803 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2785 Ų buried · 47 hydrogen bonds · protein-protein
- E–F · 2775 Ų buried · 46 hydrogen bonds · protein-protein
- G–H · 2767 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 modified (disulfide, oxidation).
Compared structures
- 5OVQ · Crystal Structure of the peroxiredoxin (AhpC2) from the Hyperthermophilic bacteria… · the same entry in another collection · chain L against L, 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 O67024
- Elsewhere: RCSB PDB 5OVQ · PDBe 5OVQ · UniProt O67024
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