MolNFT v1 · #25724 · protein
Sulfolobus solfataricus 2-keto-3-deoxygluconate (kdg) aldolase complex with D-kdgal, D-glyceraldehyde and pyruvate
1W3T · 2-keto-3-deoxy gluconate aldolase: “Sulfolobus solfataricus 2-keto-3-deoxygluconate (kdg) aldolase complex with D-kdgal, D-glyceraldehyde and…”. X-ray diffraction, 3 ligands (RSH, PYR, 3GR), 14 pockets (best druggability 0.77).…
- PDB
- 1W3T
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-keto-3-deoxy gluconate aldolase
- EC
- 4.1.2.20
- UniProt
- O54288
- Ligands
- RSH, PYR, 3GR
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-keto-3-deoxy gluconate aldolase (EC 4.1.2.20) | protein | 293 | 52% helix, 14% strand | O54288 |
Ligands and binding sites
- RSH · 3-deoxy-D-lyxo-hexonic acid · ligand · 4 copies · chains A, B, C, D
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- 3GR · D-Glyceraldehyde · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.77 | 0.89 | 40 | RSH, 3GR, GOL |
| 2 | 277 | 0.76 | 0.89 | 39 | RSH, PYR, 3GR, GOL |
| 3 | 302 | 0.76 | 0.88 | 41 | RSH, PYR, 3GR, GOL |
| 4 | 295 | 0.76 | 0.88 | 39 | RSH, PYR, 3GR, GOL |
| 5 | 268 | 0.74 | 0.88 | 37 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1746 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1744 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1138 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1130 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 1W3T · Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDGal… · 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 1W3T · PDBe 1W3T · UniProt O54288
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