Research workbench
Crystal structure of deoxyribose-phosphate aldolase from escherichia COLI (K58E-Y96W mutant) after acetaldehyde treatment and heating
Analyse Crystal structure of deoxyribose-phosphate 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
- 5EMU
- Type
- protein
- Length
- 248 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- P0A6L0
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 248 | 49% helix, 15% strand | P0A6L0 |
Ligands and binding sites
- 1BO · 1-butanol · additive · chains A
- 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
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.45 | 0.78 | 24 | 1BO |
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 5EMU · Crystal structure of deoxyribose-phosphate aldolase from Escherichia coli (K58E-Y96W… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6L0 · AlphaFold monomer V2.0 prediction for deoxyribose-phosphate aldolase (P0A6L0) · 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 P0A6L0
- Elsewhere: RCSB PDB 5EMU · PDBe 5EMU · UniProt P0A6L0
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