MolNFT v1 · #13907 · protein
Aquifex aeolicus KDO8P synthase H185G mutant in complex with pep, A5P and cadmium
1LRQ · Kdo-8-phosphate synthetase: “Aquifex aeolicus KDO8P synthase H185G mutant in complex with pep, A5P and cadmium”. X-ray diffraction, 4 ligands (PEP, A5P, CD), 5 pockets (best druggability 0.81). MolNFT v1 #13907 on GenesisL1: 3D…
- PDB
- 1LRQ
- Type
- protein
- Length
- 518 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, A5P, CD, PO4
- Pockets
- 5 · best druggability 0.81
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 | 263 | 41% helix, 21% strand | O66496 |
| B | Kdo-8-phosphate synthetase (EC 4.1.2.16) | protein | 255 | 44% helix, 19% strand | O66496 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains A
- A5P · Arabinose-5-phosphate · ligand · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.81 | 0.94 | 50 | PEP, A5P |
| 2 | 287 | 0.75 | 0.88 | 50 | PO4 |
| 3 | 72 | 0.56 | 0.88 | 29 | empty |
| 4 | 111 | 0.43 | 0.77 | 21 | empty |
| 5 | 54 | 0.28 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1906 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1LRQ · Aquifex aeolicus KDO8P synthase H185G mutant in complex with PEP, A5P 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 1LRQ · PDBe 1LRQ · UniProt O66496
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