Research workbench
Crystal structure of GDP-D-mannose dehydratase from aquifex aeolicus VF5
Analyse Crystal structure of GDP-D-mannose dehydratase from aquifex aeolicus VF5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z1M
- Type
- protein
- Length
- 1,344 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
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | GDP-D-mannose dehydratase (EC 4.2.1.47) | protein | 338 | 43% helix, 18% 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 | 336 | 43% helix, 18% strand | O67175 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.86 | 0.95 | 32 | empty |
| 2 | 386 | 0.84 | 0.93 | 57 | NDP, GDP |
| 3 | 367 | 0.84 | 0.93 | 66 | NDP, GDP |
| 4 | 810 | 0.77 | 0.80 | 71 | empty |
| 5 | 784 | 0.76 | 0.80 | 72 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1347 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1341 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1232 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 251 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2Z1M · 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 2Z1M · PDBe 2Z1M · UniProt O67175
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.