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Crystal structure of the GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP-rhamnose.
Analyse Crystal structure of the GDP-mannose 4,6-dehydratase ternary complex with NADPH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N7G
- Type
- protein
- Length
- 1,316 residues
- Chains
- 4
- 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, GDR
- Pockets
- 9 · best druggability 0.91
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-D-mannose-4,6-dehydratase (EC 4.2.1.47) | protein | 333 | 44% helix, 17% strand | P93031 |
| B | GDP-D-mannose-4,6-dehydratase (EC 4.2.1.47) | protein | 336 | 46% helix, 16% strand | P93031 |
| C | GDP-D-mannose-4,6-dehydratase (EC 4.2.1.47) | protein | 334 | 47% helix, 16% strand | P93031 |
| D | GDP-D-mannose-4,6-dehydratase (EC 4.2.1.47) | protein | 313 | 48% helix, 16% strand | P93031 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, B, D
- GDR · Guanosine-5'-diphosphate-rhamnose · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.91 | 0.93 | 143 | NDP, GDR |
| 2 | 1148 | 0.89 | 0.91 | 141 | GDR, NDP |
| 3 | 201 | 0.81 | 0.95 | 35 | empty |
| 4 | 463 | 0.63 | 0.77 | 49 | empty |
| 5 | 500 | 0.61 | 0.74 | 43 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1681 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1666 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1281 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1243 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 501 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1N7G · Crystal Structure of the GDP-mannose 4,6-dehydratase ternary complex with NADPH and… · the same entry in another collection · chain D against D, 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 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 P93031
- Elsewhere: RCSB PDB 1N7G · PDBe 1N7G · UniProt P93031
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