MolNFT v1 · #89555 · protein
Crystal structure of peroxiredoxin AHP1 from saccharomyces cerevisiae in oxidized form
4DSQ · Peroxiredoxin type-2: “Crystal structure of peroxiredoxin AHP1 from saccharomyces cerevisiae in oxidized form”. X-ray diffraction, 6 pockets (best druggability 0.75). MolNFT v1 #89555 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4DSQ
- Type
- protein
- Length
- 696 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
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peroxiredoxin type-2 (EC 1.11.1.15) | protein | 174 | 26% helix, 28% strand | P38013 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.75 | 0.85 | 62 | empty |
| 2 | 455 | 0.75 | 0.84 | 66 | empty |
| 3 | 715 | 0.71 | 0.77 | 87 | empty |
| 4 | 122 | 0.48 | 0.79 | 22 | empty |
| 5 | 88 | 0.36 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 924 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 912 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 255 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4DSQ · Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in oxidized form · 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 0.95
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 4DSQ · PDBe 4DSQ · UniProt P38013
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