Research workbench
Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant
Analyse Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H2R
- Type
- protein
- Length
- 1,171 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
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | 2-dehydro-3-deoxy-PHOSPHOGLUCONATE/2-dehydro-3-deoxy-6- phosphogalactonate aldolase (EC 4.1.2.55) | protein | 293 | 48% helix, 14% strand | O54288 |
| B | 2-dehydro-3-deoxy-PHOSPHOGLUCONATE/2-dehydro-3-deoxy-6- phosphogalactonate aldolase (EC 4.1.2.55) | protein | 292 | 50% helix, 13% strand | O54288 |
Ligands and binding sites
- IPA · Isopropyl alcohol · additive · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.74 | 0.88 | 42 | empty |
| 2 | 265 | 0.74 | 0.88 | 36 | empty |
| 3 | 280 | 0.72 | 0.86 | 44 | IPA, GOL |
| 4 | 395 | 0.72 | 0.83 | 48 | IPA, GOL |
| 5 | 408 | 0.71 | 0.82 | 51 | IPA, GOL |
Interfaces
4 interfaces between chains.
- A–B · 1678 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1579 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1196 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 1126 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6H2R · Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/A198L variant · 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 B 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 6H2R · PDBe 6H2R · UniProt O54288
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