MolNFT v1 · #112927 · protein
Crystal structure of aldose-aldose oxidoreductase from caulobacter crescentus complexed with glycerol
5A02: “Crystal structure of aldose-aldose oxidoreductase from caulobacter crescentus complexed with glycerol”. X-ray diffraction, 2 ligands (NAP, SO4), 19 pockets (best druggability 0.84). MolNFT v1 #112927 on GenesisL1: 3D structure…
- PDB
- 5A02
- Type
- protein
- Length
- 2,010 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldose-aldose oxidoreductase
- EC
- 1.1.99.-
- Ligands
- NAP, SO4
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Aldose-aldose oxidoreductase (EC 1.1.99.-) | protein | 335 | 40% helix, 23% strand | — |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, D, E
- GOL · Glycerol · additive · 16 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.84 | 0.85 | 107 | NAP, GOL |
| 2 | 907 | 0.82 | 0.84 | 67 | GOL, NAP |
| 3 | 498 | 0.73 | 0.82 | 62 | GOL |
| 4 | 446 | 0.67 | 0.79 | 31 | empty |
| 5 | 314 | 0.62 | 0.79 | 35 | GOL |
Interfaces
11 interfaces between chains.
- A–E · 1570 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1527 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 1525 Ų buried · 30 hydrogen bonds · protein-protein
- B–F · 673 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 587 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5A02 · 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 5A02 · PDBe 5A02
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