Research workbench
Escherichia COLI periplasmic aldehyde oxidase
Analyse Escherichia COLI periplasmic aldehyde oxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G5G
- Type
- protein
- Length
- 1,222 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative xanthine dehydrogenase yagt iron-sulfur-binding subunit; Putative xanthine…
- UniProt
- P77165, P77324, P77489
- Ligands
- FES, SF4, FAD, MCN, MOS, CL, IOD
- Pockets
- 7 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative xanthine dehydrogenase yagt iron-sulfur-binding subunit | protein | 175 | 37% helix, 18% strand | P77165 |
| B | Putative xanthine dehydrogenase yagr molybdenum-binding su subunit | protein | 316 | 31% helix, 20% strand | P77324 |
| C | Putative xanthine dehydrogenase yags FAD-binding subunit | protein | 731 | 30% helix, 28% strand | P77489 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, C
- SF4 · Iron/sulfur cluster · ligand · chains B
- FAD · Flavin-adenine dinucleotide · ligand · chains A, B
- MCN · Pterin cytosine dinucleotide · ligand · chains A, C
- MOS · Dioxothiomolybdenum(vi) ion · ligand · chains C
- CL · Chloride ion · ion · 12 copies · chains A, C, B
- IOD · Iodide ion · ion · 7 copies · chains A, C, B
- GOL · Glycerol · additive · 6 copies · chains A, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.90 | 0.92 | 140 | IOD, GOL, FAD, CL |
| 2 | 473 | 0.77 | 0.85 | 69 | MCN, MOS, ACT |
| 3 | 518 | 0.66 | 0.77 | 47 | empty |
| 4 | 151 | 0.52 | 0.80 | 30 | empty |
| 5 | 63 | 0.52 | 0.87 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2519 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1839 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1514 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5G5G · Escherichia coli Periplasmic Aldehyde Oxidase · the same entry in another collection · chain A against A, TM-score 1.00
- P77489 · AlphaFold monomer V2.0 prediction for aldehyde oxidoreductase molybdenum-binding subunit… · a predicted model of the same protein · chain C against A, TM-score 1.00
- P77324 · AlphaFold monomer V2.0 prediction for aldehyde oxidoreductase FAD- binding subunit paob… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P77165 · AlphaFold monomer V2.0 prediction for aldehyde oxidoreductase iron- sulfur-binding… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P77165
- Every structure of UniProt P77324
- Every structure of UniProt P77489
- Elsewhere: RCSB PDB 5G5G · PDBe 5G5G · UniProt P77165 · UniProt P77324 · UniProt P77489
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