Research workbench
Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/A198L variant in complex with L-2-keto-3DEOXY-gluconate
Analyse Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/A198L variant in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H7S
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxy-PHOSPHOGLUCONATE/2-dehydro-3-deoxy-6- phosphogalactonate aldolase
- EC
- 4.1.2.55
- UniProt
- O54288
- Ligands
- FW2
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-dehydro-3-deoxy-PHOSPHOGLUCONATE/2-dehydro-3-deoxy-6- phosphogalactonate aldolase (EC 4.1.2.55) | protein | 293 | 53% helix, 14% strand | O54288 |
Ligands and binding sites
- FW2 · L-2-keto-3deoxy-gluconate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.57 | 0.81 | 25 | FW2 |
| 2 | 191 | 0.54 | 0.79 | 30 | FW2 |
| 3 | 65 | 0.37 | 0.78 | 13 | empty |
| 4 | 55 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1093 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 6H7S · Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/A198L variant in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- O54288 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxy… · 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 O54288
- Elsewhere: RCSB PDB 6H7S · PDBe 6H7S · UniProt O54288
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