MolNFT v1 · #35569 · protein
Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase
2EF9 · 2-dehydro-3-deoxyphosphooctonate aldolase: “Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase”. X-ray diffraction, 2 ligands (PEP, A5P), 5 pockets (best druggability 0.81). MolNFT…
- PDB
- 2EF9
- Type
- protein
- Length
- 525 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
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 263 | 41% helix, 22% strand | O66496 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 262 | 42% helix, 22% strand | O66496 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- A5P · Arabinose-5-phosphate · ligand · 2 copies · chains A, 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 | 224 | 0.81 | 0.94 | 52 | PEP, A5P |
| 2 | 225 | 0.80 | 0.94 | 51 | PEP, A5P |
| 3 | 118 | 0.59 | 0.85 | 34 | empty |
| 4 | 114 | 0.42 | 0.76 | 19 | empty |
| 5 | 50 | 0.29 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1911 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2EF9 · Structural and mechanistic changes along an engineered path from metallo to non-metallo… · 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 2EF9 · PDBe 2EF9 · UniProt O66496
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