MolNFT v1 · #13904 · protein
Aquifex aeolicus KDO8P synthase H185G mutant in complex with cadmium
1LRN · Kdo-8-phosphate synthetase: “Aquifex aeolicus KDO8P synthase H185G mutant in complex with cadmium”. X-ray diffraction, 2 ligands (CD, PO4), 5 pockets (best druggability 0.77). MolNFT v1 #13904 on GenesisL1: 3D structure, binding…
- PDB
- 1LRN
- 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
- CD, PO4
- Pockets
- 5 · best druggability 0.77
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 | 43% helix, 19% strand | O66496 |
Ligands and binding sites
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 | 354 | 0.77 | 0.88 | 56 | PO4 |
| 2 | 282 | 0.72 | 0.86 | 48 | PO4 |
| 3 | 72 | 0.61 | 0.90 | 28 | empty |
| 4 | 107 | 0.42 | 0.77 | 19 | empty |
| 5 | 57 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1878 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1LRN · Aquifex aeolicus KDO8P synthase H185G mutant in complex with 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 1LRN · PDBe 1LRN · UniProt O66496
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