MolNFT v1 · #112931 · protein
Crystal structure of aldose-aldose oxidoreductase from caulobacter crescentus complexed with sorbitol
5A06: “Crystal structure of aldose-aldose oxidoreductase from caulobacter crescentus complexed with sorbitol”. X-ray diffraction, 3 ligands (SOR, NDP, SO4), 15 pockets (best druggability 0.82). MolNFT v1 #112931 on GenesisL1: 3D structure…
- PDB
- 5A06
- Type
- protein
- Length
- 2,012 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldose-aldose oxidoreductase
- EC
- 1.1.99.-
- UniProt
- Q9A8X3
- Ligands
- SOR, NDP, SO4
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aldose-aldose oxidoreductase (EC 1.1.99.-) | protein | 336 | 40% helix, 23% strand | Q9A8X3 |
| B, D, E, F | Aldose-aldose oxidoreductase (EC 1.1.99.-) | protein | 335 | 40% helix, 23% strand | Q9A8X3 |
Ligands and binding sites
- SOR · sorbitol · ligand · 19 copies · chains A, B, C, D, E, F
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.82 | 0.83 | 121 | SOR |
| 2 | 901 | 0.81 | 0.83 | 65 | NDP, SOR, SO4 |
| 3 | 1126 | 0.81 | 0.83 | 88 | SO4, NDP, SOR |
| 4 | 566 | 0.66 | 0.77 | 36 | empty |
| 5 | 419 | 0.64 | 0.78 | 27 | SOR |
Interfaces
11 interfaces between chains.
- A–E · 1590 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1541 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1532 Ų buried · 31 hydrogen bonds · protein-protein
- B–F · 614 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 586 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5A06 · Crystal structure of aldose-aldose oxidoreductase from Caulobacter crescentus complexed… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9A8X3
- Elsewhere: RCSB PDB 5A06 · PDBe 5A06 · UniProt Q9A8X3
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