Research workbench
Crystal structure of GDP-D-mannose 4,6-dehydratase in complexes with GDP and NADPH
Analyse Crystal structure of GDP-D-mannose 4,6-dehydratase in complexes with GDP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RPN
- Type
- protein
- Length
- 1,286 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose 4,6-dehydratase
- EC
- 4.2.1.47
- UniProt
- Q51366
- Ligands
- NDP, GDP
- Pockets
- 8 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GDP-mannose 4,6-dehydratase (EC 4.2.1.47) | protein | 321 | 46% helix, 17% strand | Q51366 |
| C, D | GDP-mannose 4,6-dehydratase (EC 4.2.1.47) | protein | 322 | 46% helix, 17% strand | Q51366 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, D, B, C
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.90 | 0.96 | 101 | NDP, GDP |
| 2 | 460 | 0.88 | 0.96 | 91 | NDP, GDP |
| 3 | 337 | 0.86 | 0.96 | 69 | NDP, GDP |
| 4 | 229 | 0.83 | 0.96 | 47 | NDP, GDP |
| 5 | 218 | 0.57 | 0.79 | 34 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1263 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 1259 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 1257 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1256 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 419 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1RPN · Crystal Structure of GDP-D-mannose 4,6-dehydratase in complexes with GDP and NADPH · the same entry in another collection · chain A against A, TM-score 1.00
- Q51366 · AlphaFold monomer V2.0 prediction for GDP-mannose 4,6-dehydratase (Q51366) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q51366
- Elsewhere: RCSB PDB 1RPN · PDBe 1RPN · UniProt Q51366
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