Research workbench
2-dehydro-3-deoxy-galactarate aldolase from escherichia COLI
Analyse 2-dehydro-3-deoxy-galactarate aldolase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DXE
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxy-galactarate aldolase
- EC
- 4.1.2.20
- UniProt
- P23522
- Ligands
- MG, PO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-dehydro-3-deoxy-galactarate aldolase (EC 4.1.2.20) | protein | 253 | 44% helix, 16% strand | P23522 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.61 | 0.79 | 29 | empty |
| 2 | 253 | 0.59 | 0.79 | 22 | empty |
| 3 | 164 | 0.44 | 0.75 | 33 | PO4, MG |
| 4 | 128 | 0.41 | 0.75 | 35 | PO4, MG |
| 5 | 57 | 0.26 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1514 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1DXE · 2-dehydro-3-deoxy-galactarate aldolase from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
- P23522 · AlphaFold monomer V2.0 prediction for 5-keto-4-deoxy-D-glucarate aldolase (P23522) · 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 P23522
- Elsewhere: RCSB PDB 1DXE · PDBe 1DXE · UniProt P23522
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