MolNFT v1 · #150739 · protein
Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant, pyruvate complex
6H2S · 2-dehydro-3-deoxy-PHOSPHOGLUCONATE/2-dehydro-3-deoxy-6…: “Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant, pyruvate complex”. X-ray diffraction, 1 ligand (PYR), 10 pockets (best druggability 0.74).…
- PDB
- 6H2S
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- 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
- PYR
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2-dehydro-3-deoxy-PHOSPHOGLUCONATE/2-dehydro-3-deoxy-6- phosphogalactonate aldolase (EC 4.1.2.55) | protein | 293 | 50% helix, 14% strand | O54288 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, C, D
- IPA · Isopropyl alcohol · additive · chains A
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 | 371 | 0.74 | 0.85 | 48 | PYR, GOL |
| 2 | 268 | 0.74 | 0.88 | 36 | empty |
| 3 | 244 | 0.74 | 0.88 | 35 | PYR |
| 4 | 395 | 0.73 | 0.84 | 50 | PYR, GOL |
| 5 | 276 | 0.73 | 0.87 | 40 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1700 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1678 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1201 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1184 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6H2S · Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant… · the same entry in another collection · chain B against B, 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 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 O54288
- Elsewhere: RCSB PDB 6H2S · PDBe 6H2S · UniProt O54288
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