Research workbench
Crystal structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP
Analyse Crystal structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N7H
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-D-mannose-4,6-dehydratase
- EC
- 4.2.1.47
- UniProt
- P93031
- Ligands
- NDP, GDP
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-D-mannose-4,6-dehydratase (EC 4.2.1.47) | protein | 331 | 46% helix, 17% strand | P93031 |
| B | GDP-D-mannose-4,6-dehydratase (EC 4.2.1.47) | protein | 334 | 47% helix, 17% strand | P93031 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.81 | 0.86 | 69 | NDP, GDP |
| 2 | 667 | 0.80 | 0.85 | 73 | NDP, GDP |
| 3 | 227 | 0.53 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1289 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1N7H · Crystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP · the same entry in another collection · chain A against A, TM-score 1.00
- P93031 · AlphaFold monomer V2.0 prediction for GDP-mannose 4,6 dehydratase 2 (P93031) · a predicted model of the same protein · 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 P93031
- Elsewhere: RCSB PDB 1N7H · PDBe 1N7H · UniProt P93031
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.