MolNFT v1 · #56244 · protein
Crystal structure of GDP-D-mannose dehydratase from aquifex aeolicus VF5
2Z95: “Crystal structure of GDP-D-mannose dehydratase from aquifex aeolicus VF5”. X-ray diffraction, 2 ligands (NDP, GDP), 11 pockets (best druggability 0.87). MolNFT v1 #56244 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Z95
- Type
- protein
- Length
- 1,335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-D-mannose dehydratase
- EC
- 4.2.1.47
- UniProt
- O67175
- Ligands
- NDP, GDP
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-D-mannose dehydratase (EC 4.2.1.47) | protein | 333 | 42% helix, 19% strand | O67175 |
| B | GDP-D-mannose dehydratase (EC 4.2.1.47) | protein | 332 | 44% helix, 18% strand | O67175 |
| C | GDP-D-mannose dehydratase (EC 4.2.1.47) | protein | 338 | 42% helix, 18% strand | O67175 |
| D | GDP-D-mannose dehydratase (EC 4.2.1.47) | protein | 332 | 41% helix, 18% strand | O67175 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.87 | 0.88 | 117 | GDP |
| 2 | 345 | 0.86 | 0.95 | 31 | empty |
| 3 | 1088 | 0.78 | 0.80 | 80 | NDP |
| 4 | 1171 | 0.76 | 0.78 | 80 | empty |
| 5 | 289 | 0.60 | 0.79 | 39 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1339 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1283 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1015 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 537 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 319 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2Z95 · Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5 · the same entry in another collection · 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 O67175
- Elsewhere: RCSB PDB 2Z95 · PDBe 2Z95 · UniProt O67175
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