Research workbench
2-keto-3-deoxygluconate kinase from thermus thermophilus
Analyse 2-keto-3-deoxygluconate kinase from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V19
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-keto-3-deoxygluconate kinase
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-keto-3-deoxygluconate kinase | protein | 301 | 39% helix, 24% strand | — |
Ligands and binding sites
- DIO · 1,4-diethylene dioxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.70 | 0.79 | 58 | empty |
| 2 | 592 | 0.69 | 0.78 | 61 | empty |
| 3 | 184 | 0.45 | 0.74 | 31 | DIO |
| 4 | 81 | 0.37 | 0.77 | 13 | empty |
| 5 | 86 | 0.36 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1184 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1V19 · 2-keto-3-deoxygluconate kinase from thermus thermophilus · 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
- Elsewhere: RCSB PDB 1V19 · PDBe 1V19
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.