Research workbench
Sulfolobus sulfataricus 2-keto-3-deoxygluconate aldolase Y103F,Y130F, A198F variant
Analyse Sulfolobus sulfataricus 2-keto-3-deoxygluconate aldolase Y103F,Y130F, A198F… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YDA
- Type
- protein
- Length
- 585 residues
- Chains
- 2
- 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
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-keto-3-deoxy gluconate aldolase (EC 4.1.2.20) | protein | 292 | 52% helix, 13% strand | O54288 |
| B | 2-keto-3-deoxy gluconate aldolase (EC 4.1.2.20) | protein | 293 | 53% helix, 14% strand | O54288 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.56 | 0.79 | 32 | empty |
| 2 | 190 | 0.55 | 0.79 | 31 | IPA |
| 3 | 55 | 0.39 | 0.81 | 13 | empty |
| 4 | 52 | 0.38 | 0.80 | 14 | empty |
| 5 | 57 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2YDA · Sulfolobus sulfataricus 2-keto-3-deoxygluconate aldolase Y103F,Y130F, A198F 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 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 2YDA · PDBe 2YDA · UniProt O54288
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