Research workbench
Observation of covalent intermediates in an enzyme mechanism at atomic resolution
Analyse Observation of covalent intermediates in an enzyme mechanism at atomic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JCJ
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- P0A6L0
- Ligands
- HPD
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 252 | 49% helix, 15% strand | P0A6L0 |
| B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 251 | 49% helix, 15% strand | P0A6L0 |
Ligands and binding sites
- HPD · 1-hydroxy-pentane-3,4-diol-5-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.76 | 0.82 | 57 | empty |
| 2 | 80 | 0.52 | 0.85 | 19 | HPD |
| 3 | 76 | 0.50 | 0.84 | 21 | HPD |
Interfaces
1 interface between chains.
- A–B · 622 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1JCJ · Observation of covalent intermediates in an enzyme mechanism at atomic resolution · 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 B 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 P0A6L0
- Elsewhere: RCSB PDB 1JCJ · PDBe 1JCJ · UniProt P0A6L0
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