MolNFT v1 · #112928 · protein
Crystal structure of aldose-aldose oxidoreductase from caulobacter crescentus complexed with xylose
5A03: “Crystal structure of aldose-aldose oxidoreductase from caulobacter crescentus complexed with xylose”. X-ray diffraction, 4 ligands (NDP, XYP, XYS), 15 pockets (best druggability 0.84). MolNFT v1 #112928 on GenesisL1: 3D structure…
- PDB
- 5A03
- Type
- protein
- Length
- 2,011 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldose-aldose oxidoreductase
- EC
- 1.1.99.-
- Ligands
- NDP, XYP, XYS, SO4
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Aldose-aldose oxidoreductase (EC 1.1.99.-) | protein | 335 | 40% helix, 23% strand | — |
| C | Aldose-aldose oxidoreductase (EC 1.1.99.-) | protein | 336 | 40% helix, 23% strand | — |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- XYP · beta-D-xylopyranose · sugar · 13 copies · chains A, F, B, C, D, E
- XYS · alpha-D-xylopyranose · sugar · 2 copies · chains B, D, E
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, D, E, F
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.84 | 0.85 | 112 | NDP, XYP, XYS, SO4 |
| 2 | 951 | 0.82 | 0.83 | 68 | NDP, XYP |
| 3 | 725 | 0.78 | 0.83 | 92 | NDP, XYP |
| 4 | 551 | 0.64 | 0.76 | 57 | XYP |
| 5 | 406 | 0.63 | 0.78 | 37 | empty |
Interfaces
11 interfaces between chains.
- B–D · 1567 Ų buried · 34 hydrogen bonds · protein-protein
- C–F · 1562 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 1562 Ų buried · 34 hydrogen bonds · protein-protein
- B–F · 573 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 520 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5A03 · 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
- Elsewhere: RCSB PDB 5A03 · PDBe 5A03
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