MolNFT v1 · #112929 · protein
Crystal structure of aldose-aldose oxidoreductase from caulobacter crescentus complexed with glucose
5A04: “Crystal structure of aldose-aldose oxidoreductase from caulobacter crescentus complexed with glucose”. X-ray diffraction, 3 ligands (NDP, BGC, SO4), 17 pockets (best druggability 0.84). MolNFT v1 #112929 on GenesisL1: 3D structure…
- PDB
- 5A04
- 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
- NDP, BGC, SO4
- Pockets
- 17 · 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
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- BGC · beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
- DIO · 1,4-diethylene dioxide · additive · 5 copies · chains A, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.84 | 0.85 | 111 | NDP, BGC, SO4, DIO |
| 2 | 1007 | 0.81 | 0.82 | 66 | NDP, BGC |
| 3 | 372 | 0.74 | 0.85 | 49 | empty |
| 4 | 386 | 0.62 | 0.78 | 33 | SO4 |
| 5 | 234 | 0.62 | 0.81 | 30 | NDP, BGC |
Interfaces
11 interfaces between chains.
- A–E · 1571 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 1548 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1541 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 567 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 562 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5A04 · 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 5A04 · PDBe 5A04
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