MolNFT v1 · #14646 · protein
Partially refined 2.8 a crystal structure of GDP-mannose dehydrogenase from P. aeruginosa
1MFZ · GDP-mannose 6-dehydrogenase: “Partially refined 2.8 a crystal structure of GDP-mannose dehydrogenase from P. aeruginosa”. X-ray diffraction, 1 ligand (GDX), 8 pockets (best druggability 0.80). MolNFT v1 #14646 on GenesisL1: 3D…
- PDB
- 1MFZ
- Type
- protein
- Length
- 1,744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose 6-dehydrogenase
- EC
- 1.1.1.132
- UniProt
- P11759
- Ligands
- GDX
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | GDP-mannose 6-dehydrogenase (EC 1.1.1.132) | protein | 436 | 46% helix, 14% strand | P11759 |
Ligands and binding sites
- GDX · Guanosine 5'-(trihydrogen diphosphate), P'-D-mannopyranosyl ester · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.80 | 0.83 | 78 | GDX |
| 2 | 877 | 0.80 | 0.83 | 81 | GDX |
| 3 | 856 | 0.79 | 0.82 | 83 | GDX |
| 4 | 431 | 0.79 | 0.87 | 40 | GDX |
| 5 | 59 | 0.70 | 0.97 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 6191 Ų buried · 77 hydrogen bonds · protein-protein
- C–D · 6098 Ų buried · 83 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 1MFZ · Partially refined 2.8 A Crystal structure of GDP-mannose dehydrogenase from P. aeruginosa · the same entry in another collection · chain D against D, TM-score 1.00
- P11759 · AlphaFold monomer V2.0 prediction for GDP-mannose 6-dehydrogenase (P11759) · a predicted model of the same protein · chain D 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 P11759
- Elsewhere: RCSB PDB 1MFZ · PDBe 1MFZ · UniProt P11759
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