MolNFT v1 · #119745 · protein
Escherichia COLI periplasmic aldehyde oxidase R440H mutant
5G5H · Putative xanthine dehydrogenase yagt iron-sulfur-binding…: “Escherichia COLI periplasmic aldehyde oxidase R440H mutant”. X-ray diffraction, 8 ligands (FES, SF4, FAD), 7 pockets (best druggability 0.89). MolNFT v1 #119745 on…
- PDB
- 5G5H
- Type
- protein
- Length
- 1,218 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…
- EC
- 1.17.1.4
- UniProt
- P77165, P77324, P77489
- Ligands
- FES, SF4, FAD, CSD, MCN, MOS, CL, IOD
- Pockets
- 7 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative xanthine dehydrogenase yagt iron-sulfur-binding subunit | protein | 173 | 36% helix, 18% strand | P77165 |
| B | Putative xanthine dehydrogenase yags FAD-binding subunit (EC 1.17.1.4) | protein | 316 | 30% helix, 20% strand | P77324 |
| C | Putative xanthine dehydrogenase yagr molybdenum-binding subunit (EC 1.17.1.4) | protein | 729 | 28% helix, 27% 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
- CSD · 3-sulfinoalanine · ligand · chains C
- MCN · Pterin cytosine dinucleotide · ligand · chains A, C
- MOS · Dioxothiomolybdenum(vi) ion · ligand · chains C
- CL · Chloride ion · ion · 10 copies · chains A, B, C
- IOD · Iodide ion · ion · 8 copies · chains A, C, B
- ACT · Acetate ion · additive · 3 copies · chains A, C
- GOL · Glycerol · additive · 3 copies · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.89 | 0.91 | 156 | IOD, FAD, CL, ACT |
| 2 | 479 | 0.77 | 0.85 | 73 | MCN, MOS, GOL |
| 3 | 61 | 0.69 | 0.96 | 21 | empty |
| 4 | 496 | 0.65 | 0.77 | 43 | empty |
| 5 | 130 | 0.48 | 0.79 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2502 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1844 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1467 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5G5H · Escherichia coli Periplasmic Aldehyde Oxidase R440H mutant · the same entry in another collection · chain B against B, 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 5G5H · PDBe 5G5H · UniProt P77165 · UniProt P77324 · UniProt P77489
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