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Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) in complex with GDP-Man
Analyse Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GPK
- Type
- protein
- Length
- 1,386 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.47
- Source
- Homo sapiens
- Molecule
- GDP-mannose 4,6 dehydratase
- EC
- 4.2.1.47
- UniProt
- O60547
- Ligands
- NAP, GDD
- Pockets
- 12 · best druggability 0.91
Structure
x-ray diffraction · resolution 1.47 · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GDP-mannose 4,6 dehydratase (EC 4.2.1.47) | protein | 350 | 41% helix, 19% strand | O60547 |
| C | GDP-mannose 4,6 dehydratase (EC 4.2.1.47) | protein | 342 | 42% helix, 19% strand | O60547 |
| D | GDP-mannose 4,6 dehydratase (EC 4.2.1.47) | protein | 344 | 42% helix, 19% strand | O60547 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.91 | 0.93 | 132 | EDO, NAP, GDD |
| 2 | 1186 | 0.91 | 0.93 | 136 | EDO, NAP, GDD |
| 3 | 334 | 0.84 | 0.93 | 34 | EDO |
| 4 | 244 | 0.71 | 0.86 | 38 | empty |
| 5 | 191 | 0.68 | 0.87 | 25 | EDO |
Interfaces
6 interfaces between chains.
- A–B · 1807 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1261 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1252 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1251 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 272 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6GPK · Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) in complex with GDP-man · 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 C 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 6GPK · PDBe 6GPK · UniProt O60547
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