Research workbench
Crystal structure of peroxiredoxin-like protein from aquifex aeolicus
Analyse Crystal structure of peroxiredoxin-like protein from aquifex aeolicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YZH
- Type
- protein
- Length
- 681 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable thiol peroxidase
- EC
- 1.11.1.-
- UniProt
- O66780
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Probable thiol peroxidase (EC 1.11.1.-) | protein | 170 | 22% helix, 31% strand | O66780 |
| D | Probable thiol peroxidase (EC 1.11.1.-) | protein | 171 | 23% helix, 30% strand | O66780 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.85 | 0.94 | 36 | empty |
| 2 | 216 | 0.50 | 0.76 | 34 | SO4 |
| 3 | 196 | 0.49 | 0.76 | 30 | empty |
| 4 | 174 | 0.47 | 0.76 | 25 | empty |
| 5 | 159 | 0.46 | 0.76 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–D · 920 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 916 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 448 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 425 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 419 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 O66780
- Elsewhere: RCSB PDB 2YZH · PDBe 2YZH · UniProt O66780
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