MolNFT v1 · #22564 · protein
R106G KDO8PS with pep and A5P
1T8X · 2-dehydro-3-deoxyphosphooctonate aldolase: “R106G KDO8PS with pep and A5P”. X-ray diffraction, 4 ligands (PEP, A5P, CD), 5 pockets (best druggability 0.79). MolNFT v1 #22564 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1T8X
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 2.5.1.55
- UniProt
- O66496
- Ligands
- PEP, A5P, CD, PO4
- Pockets
- 5 · best druggability 0.79
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 2.5.1.55) | protein | 257 | 42% helix, 20% strand | O66496 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 256 | 43% helix, 20% strand | O66496 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- A5P · Arabinose-5-phosphate · ligand · chains A
- CD · Cadmium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
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 | 397 | 0.79 | 0.88 | 48 | PO4, PEP |
| 2 | 388 | 0.78 | 0.88 | 48 | PEP, A5P |
| 3 | 79 | 0.56 | 0.87 | 30 | empty |
| 4 | 114 | 0.43 | 0.77 | 22 | empty |
| 5 | 58 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1702 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1T8X · r106g kdo8ps with pep and a5p · the same entry in another collection · 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 1T8X · PDBe 1T8X · UniProt O66496
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