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Crystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex with GDP-man
Analyse Crystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q94
- Type
- protein
- Length
- 2,776 residues
- Chains
- 8
- 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, GDD
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | GDP-mannose 4,6 dehydratase (EC 4.2.1.47) | protein | 344 | 41% helix, 19% strand | O60547 |
| A, E, F, G | 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 | 348 | 41% helix, 19% strand | O60547 |
| D | GDP-mannose 4,6 dehydratase (EC 4.2.1.47) | protein | 343 | 41% helix, 19% strand | O60547 |
| H | GDP-mannose 4,6 dehydratase (EC 4.2.1.47) | protein | 341 | 42% helix, 19% strand | O60547 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains B, A, C, E, D, F, G, H
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 8 copies · chains B, A, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 4 copies · chains D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.91 | 0.93 | 139 | NAP, GDD |
| 2 | 1153 | 0.91 | 0.93 | 137 | NAP, GDD |
| 3 | 1124 | 0.91 | 0.93 | 133 | NAP, GDD |
| 4 | 1198 | 0.91 | 0.93 | 138 | NAP, GDD |
| 5 | 332 | 0.84 | 0.94 | 37 | empty |
Interfaces
14 interfaces between chains.
- G–H · 1607 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1437 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1436 Ų buried · 19 hydrogen bonds · protein-protein
- B–A · 1394 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1289 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6Q94 · Crystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex with GDP-Man · the same entry in another collection · chain H against H, 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 B 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 6Q94 · PDBe 6Q94 · UniProt O60547
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