MolNFT v1 · #28465 · protein
Structural and biochemical analysis of the link between enzymatic activity and oligomerization in ahpc, a bacterial peroxiredoxin.
1YF1 · Alkyl hydroperoxide reductase subunit C: “Structural and biochemical analysis of the link between enzymatic activity and oligomerization in ahpc, a…”. X-ray diffraction, 1 ligand (NA), 20 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 1YF1
- Type
- protein
- Length
- 1,650 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyl hydroperoxide reductase subunit C
- EC
- 1.11.1.15
- UniProt
- P0A251
- Ligands
- NA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, I | Alkyl hydroperoxide reductase subunit C (EC 1.11.1.15) | protein | 166 | 30% helix, 29% strand | P0A251 |
| B, E, G, J | Alkyl hydroperoxide reductase subunit C (EC 1.11.1.15) | protein | 165 | 32% helix, 28% strand | P0A251 |
| C, H | Alkyl hydroperoxide reductase subunit C (EC 1.11.1.15) | protein | 163 | 31% helix, 29% strand | P0A251 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
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 | 1091 | 0.78 | 0.80 | 95 | empty |
| 2 | 1176 | 0.78 | 0.80 | 102 | empty |
| 3 | 107 | 0.69 | 0.91 | 18 | empty |
| 4 | 89 | 0.64 | 0.90 | 18 | empty |
| 5 | 69 | 0.61 | 0.90 | 17 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1244 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 1223 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1209 Ų buried · 18 hydrogen bonds · protein-protein
- H–I · 1199 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 666 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1YF1 · Structural and biochemical analysis of the link between enzymatic activity and… · the same entry in another collection · chain J against J, TM-score 1.00
- P0A251 · AlphaFold monomer V2.0 prediction for alkyl hydroperoxide reductase C (P0A251) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P0A251
- Elsewhere: RCSB PDB 1YF1 · PDBe 1YF1 · UniProt P0A251
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