MolNFT v1 · #28464 · protein
Structural and biochemical analysis of the link between enzymatic activity and oligomerization in ahpc, a bacterial peroxiredoxin.
1YF0 · 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 (SO4), 11 pockets (best druggability 0.69). MolNFT v1…
- PDB
- 1YF0
- Type
- protein
- Length
- 826 residues
- Chains
- 5
- 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
- SO4
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkyl hydroperoxide reductase subunit C (EC 1.11.1.15) | protein | 167 | 32% helix, 28% strand | P0A251 |
| B, E | Alkyl hydroperoxide reductase subunit C (EC 1.11.1.15) | protein | 165 | 31% helix, 30% strand | P0A251 |
| C | Alkyl hydroperoxide reductase subunit C (EC 1.11.1.15) | protein | 163 | 31% helix, 29% strand | P0A251 |
| D | Alkyl hydroperoxide reductase subunit C (EC 1.11.1.15) | protein | 166 | 31% helix, 29% strand | P0A251 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.69 | 0.90 | 21 | empty |
| 2 | 79 | 0.62 | 0.90 | 17 | empty |
| 3 | 255 | 0.59 | 0.79 | 45 | SO4 |
| 4 | 347 | 0.58 | 0.76 | 56 | SO4 |
| 5 | 63 | 0.54 | 0.88 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1267 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1108 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 665 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 659 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1YF0 · Structural and biochemical analysis of the link between enzymatic activity and… · the same entry in another collection · chain E against E, 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 1YF0 · PDBe 1YF0 · UniProt P0A251
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