Research workbench
Crystal structure of GDP-mannose 4,6 dehydratase in complex with natural inhibitor GDP-fucose
Analyse Crystal structure of GDP-mannose 4,6 dehydratase in complex with natural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IN5
- Type
- protein
- Length
- 1,408 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
- O60547
- Ligands
- NAP, GDP, GFB
- Pockets
- 11 · best druggability 0.91
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | GDP-mannose 4,6 dehydratase (EC 4.2.1.47) | protein | 351 | 41% helix, 19% strand | O60547 |
| C | GDP-mannose 4,6 dehydratase (EC 4.2.1.47) | protein | 355 | 41% helix, 19% strand | O60547 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- GFB · Guanosine-5'-diphosphate-beta-L-fucopyranose · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.91 | 0.94 | 144 | NAP, GDP |
| 2 | 1058 | 0.87 | 0.88 | 102 | GFB, NAP, GDP |
| 3 | 1068 | 0.86 | 0.88 | 108 | NAP, GDP, GFB |
| 4 | 223 | 0.82 | 0.95 | 38 | empty |
| 5 | 216 | 0.56 | 0.79 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1822 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1796 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1279 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1228 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 287 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IN5 · Crystal Structure of GDP-mannose 4,6 dehydratase in complex with natural inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- O60547 · AlphaFold monomer V2.0 prediction for GDP-mannose 4,6 dehydratase (O60547) · 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 O60547
- Elsewhere: RCSB PDB 5IN5 · PDBe 5IN5 · UniProt O60547
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