Research workbench
Crystal structure of the alkylhydroperoxide reductase ahpf from escherichia COLI
Analyse Crystal structure of the alkylhydroperoxide reductase ahpf from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O5Q
- 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
- UniProt
- P35340
- Ligands
- FAD, CD, SO4
- Pockets
- 6 · best druggability 0.77
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 | protein | 521 | 32% helix, 25% strand | P35340 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- CD · Cadmium ion · metal · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
- GOL · Glycerol · additive · 7 copies · chains A
- PGE · Triethylene glycol · additive · 6 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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 | 514 | 0.77 | 0.84 | 55 | FAD, GOL |
| 2 | 248 | 0.57 | 0.78 | 24 | SO4, PGE |
| 3 | 114 | 0.41 | 0.76 | 25 | empty |
| 4 | 72 | 0.35 | 0.76 | 17 | empty |
| 5 | 61 | 0.30 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4O5Q · Crystal Structure of the Alkylhydroperoxide Reductase AhpF from Escherichia coli · 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 0.63
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 4O5Q · PDBe 4O5Q · UniProt P35340
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