Research workbench
Aquifex aeolicus KDO8P synthase in complex with R5P, pep and cadmium
Analyse Aquifex aeolicus KDO8P synthase in complex with R5P, pep and cadmium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JCY
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 4.1.2.16
- UniProt
- O66496
- Ligands
- PEP, R5P, CD, PO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 4.1.2.16) | protein | 263 | 41% helix, 21% strand | O66496 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 4.1.2.16) | protein | 255 | 42% helix, 19% strand | O66496 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- R5P · Ribose-5-phosphate · ligand · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.77 | 0.92 | 38 | R5P, PEP |
| 2 | 307 | 0.74 | 0.87 | 48 | PO4, PEP |
| 3 | 73 | 0.63 | 0.91 | 25 | empty |
| 4 | 102 | 0.42 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1907 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1JCY · Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium · the same entry in another collection · chain A against A, TM-score 1.00
- O66496 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (O66496) · 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 O66496
- Elsewhere: RCSB PDB 1JCY · PDBe 1JCY · UniProt O66496
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