Research workbench
Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase
Analyse Structural and mechanistic changes along an engineered path from metallo to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NX3
- Type
- protein
- Length
- 3,144 residues
- Chains
- 12
- 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, 1NT
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 262 | 44% helix, 21% strand | O66496 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 11 copies · chains A, B, C, E, F, G, H, I, J, K, L
- A5P · Arabinose-5-phosphate · ligand · 11 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 1NT · (2R,4R,5R,6R,7R)-2,4,5,6,7-pentahydroxy-2,8-bis(phosphonooxy)octanoic acid · ligand · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.81 | 0.94 | 54 | PEP, A5P |
| 2 | 190 | 0.80 | 0.95 | 53 | PEP, A5P |
| 3 | 222 | 0.80 | 0.94 | 52 | PEP, A5P |
| 4 | 206 | 0.80 | 0.94 | 49 | PEP, A5P |
| 5 | 213 | 0.80 | 0.94 | 50 | PEP, A5P |
Interfaces
24 interfaces between chains.
- A–B · 1922 Ų buried · 31 hydrogen bonds · protein-protein
- I–J · 1922 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1906 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1900 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1899 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 2NX3 · 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 2NX3 · PDBe 2NX3 · UniProt O66496
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