Research workbench
Crystal structure of 2-keto-3-deoxygluconate kinase (form 1) from sulfolobus tokodaii
Analyse Crystal structure of 2-keto-3-deoxygluconate kinase (form 1) from sulfolobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WYE
- Type
- protein
- Length
- 1,854 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-keto-3-deoxygluconate kinase
- EC
- 2.7.1.45
- UniProt
- Q96XN9
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 2-keto-3-deoxygluconate kinase (EC 2.7.1.45) | protein | 309 | 40% helix, 25% strand | Q96XN9 |
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.85 | 0.93 | 45 | empty |
| 2 | 409 | 0.84 | 0.93 | 45 | empty |
| 3 | 386 | 0.84 | 0.93 | 47 | empty |
| 4 | 637 | 0.76 | 0.82 | 61 | empty |
| 5 | 606 | 0.76 | 0.82 | 58 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1204 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1190 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1189 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 617 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 614 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1WYE · Crystal structure of 2-keto-3-deoxygluconate kinase (form 1) from Sulfolobus Tokodaii · the same entry in another collection · chain C against C, TM-score 1.00
- Q96XN9 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxygluconokinase (Q96XN9) · a predicted model of the same protein · chain A 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 Q96XN9
- Elsewhere: RCSB PDB 1WYE · PDBe 1WYE · UniProt Q96XN9
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