Research workbench
Crystal structure of AHP1 from saccharomyces cerevisiae. investigating the electron transfers.
Analyse Crystal structure of AHP1 from saccharomyces cerevisiae. investigating the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OWY
- Type
- protein
- Length
- 686 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin type-2
- EC
- 1.11.1.15
- UniProt
- P38013
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxiredoxin type-2 (EC 1.11.1.15) | protein | 169 | 25% helix, 28% strand | P38013 |
| B, D | Peroxiredoxin type-2 (EC 1.11.1.15) | protein | 174 | 26% helix, 28% strand | P38013 |
| C | Peroxiredoxin type-2 (EC 1.11.1.15) | protein | 169 | 24% helix, 27% strand | P38013 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, B
- ACY · Acetic acid · additive · 4 copies · chains A, B, C, D
- TBU · Tertiary-butyl alcohol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.75 | 0.81 | 89 | PEG |
| 2 | 238 | 0.63 | 0.82 | 47 | empty |
| 3 | 242 | 0.55 | 0.77 | 40 | empty |
| 4 | 73 | 0.45 | 0.81 | 22 | empty |
| 5 | 103 | 0.44 | 0.79 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 842 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 806 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 256 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 145 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4OWY · Crystal Structure of Ahp1 from Saccharomyces cerevisiae. Investigating the electron… · the same entry in another collection · chain D against D, TM-score 1.00
- P38013 · AlphaFold monomer V2.0 prediction for peroxiredoxin AHP1 (P38013) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P38013
- Elsewhere: RCSB PDB 4OWY · PDBe 4OWY · UniProt P38013
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