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
- 2NXG
- Type
- protein
- Length
- 518 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, 1NT
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 263 | 41% helix, 21% strand | O66496 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 255 | 44% helix, 20% strand | O66496 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains A
- A5P · Arabinose-5-phosphate · ligand · chains A, B
- 1NT · (2R,4R,5R,6R,7R)-2,4,5,6,7-pentahydroxy-2,8-bis(phosphonooxy)octanoic acid · ligand · 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 | 213 | 0.80 | 0.94 | 48 | PEP, A5P |
| 2 | 256 | 0.75 | 0.88 | 47 | 1NT |
| 3 | 89 | 0.57 | 0.86 | 29 | empty |
| 4 | 106 | 0.42 | 0.77 | 22 | empty |
| 5 | 67 | 0.30 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1897 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2NXG · 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 2NXG · PDBe 2NXG · UniProt O66496
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