MolNFT v1 · #111221 · protein
Crystal structure of the alkylhydroperoxide reductase subunit F (ahpf) with NAD+ from escherichia COLI
4YKG · Alkyl hydroperoxide reductase subunit F: “Crystal structure of the alkylhydroperoxide reductase subunit F (ahpf) with NAD+ from escherichia COLI”. X-ray diffraction, 4 ligands (FAD, NAD, CD), 6 pockets (best druggability 0.76).…
- PDB
- 4YKG
- Type
- protein
- Length
- 521 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyl hydroperoxide reductase subunit F
- EC
- 1.8.1.-
- UniProt
- P35340
- Ligands
- FAD, NAD, CD, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkyl hydroperoxide reductase subunit F (EC 1.8.1.-) | protein | 521 | 32% helix, 25% strand | P35340 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- CD · Cadmium ion · metal · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A
- GOL · Glycerol · additive · 6 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.76 | 0.83 | 58 | FAD, GOL |
| 2 | 219 | 0.52 | 0.76 | 24 | NAD |
| 3 | 91 | 0.42 | 0.78 | 17 | empty |
| 4 | 102 | 0.41 | 0.77 | 20 | empty |
| 5 | 68 | 0.35 | 0.76 | 14 | NAD |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, oxidation).
Compared structures
- 4YKG · Crystal Structure of the Alkylhydroperoxide Reductase subunit F (AhpF) with NAD+ from… · the same entry in another collection · chain A against A, TM-score 1.00
- P35340 · AlphaFold monomer V2.0 prediction for alkyl hydroperoxide reductase subunit F (P35340) · a predicted model of the same protein · chain A against A, TM-score 0.64
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 P35340
- Elsewhere: RCSB PDB 4YKG · PDBe 4YKG · UniProt P35340
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