Research workbench
Aquifex aeolicus KDO8P synthase in complex with api and cadmium
Analyse Aquifex aeolicus KDO8P synthase in complex with api and cadmium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JCX
- Type
- protein
- Length
- 509 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
- PAI, CD
- Pockets
- 6 · best druggability 0.72
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 | 255 | 41% helix, 20% strand | O66496 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 4.1.2.16) | protein | 254 | 44% helix, 20% strand | O66496 |
Ligands and binding sites
- PAI · {[(2,2-dihydroxy-ethyl)-(2,3,4,5-tetrahydroxy-6-phosphonooxy-hexyl)-amino]-methyl}-phosphonic acid · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.72 | 0.86 | 48 | PAI |
| 2 | 319 | 0.72 | 0.85 | 47 | PAI |
| 3 | 91 | 0.58 | 0.87 | 31 | empty |
| 4 | 60 | 0.34 | 0.77 | 12 | empty |
| 5 | 54 | 0.29 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1828 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1JCX · Aquifex aeolicus KDO8P synthase in complex with API 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 1JCX · PDBe 1JCX · UniProt O66496
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