MolNFT v1 · #58613 · protein
Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (cold) H188N mutant with bound GDP-perosamine
3B8X · Pyridoxamine 5-phosphate-dependent dehydrase: “Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (cold) H188N mutant with bound GDP-perosamine”. X-ray diffraction, 2 ligands (G4M, NA), 7 pockets (best druggability 0.75).…
- PDB
- 3B8X
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxamine 5-phosphate-dependent dehydrase
- UniProt
- Q9F118
- Ligands
- G4M, NA
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxamine 5-phosphate-dependent dehydrase | protein | 386 | 37% helix, 19% strand | Q9F118 |
| B | Pyridoxamine 5-phosphate-dependent dehydrase | protein | 388 | 38% helix, 19% strand | Q9F118 |
Ligands and binding sites
- G4M · [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
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 | 323 | 0.75 | 0.87 | 43 | NA, G4M |
| 2 | 410 | 0.72 | 0.83 | 53 | EDO, G4M |
| 3 | 59 | 0.70 | 0.98 | 22 | empty |
| 4 | 221 | 0.59 | 0.80 | 27 | empty |
| 5 | 85 | 0.43 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2697 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3B8X · Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase (ColD) H188N mutant with… · 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 Q9F118
- Elsewhere: RCSB PDB 3B8X · PDBe 3B8X · UniProt Q9F118
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