Research workbench
Aquifex aeolicus KDO8P synthase H185G mutant in complex with pep and cadmium
Analyse Aquifex aeolicus KDO8P synthase H185G mutant in complex with 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
- 1LRO
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kdo-8-phosphate synthetase
- EC
- 4.1.2.16
- UniProt
- O66496
- Ligands
- PEP, CD, PO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kdo-8-phosphate synthetase (EC 4.1.2.16) | protein | 259 | 42% helix, 20% strand | O66496 |
| B | Kdo-8-phosphate synthetase (EC 4.1.2.16) | protein | 254 | 42% helix, 19% strand | O66496 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · 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 | 322 | 0.75 | 0.87 | 52 | PO4, PEP |
| 2 | 285 | 0.75 | 0.88 | 49 | PO4, PEP |
| 3 | 65 | 0.61 | 0.91 | 25 | empty |
| 4 | 115 | 0.43 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1890 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1LRO · Aquifex aeolicus KDO8P synthase H185G mutant in complex with 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 1LRO · PDBe 1LRO · UniProt O66496
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