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
- 2NXI
- Type
- protein
- Length
- 3,091 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, PO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 257 | 44% helix, 19% strand | O66496 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 258 | 43% helix, 19% strand | O66496 |
| C | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 257 | 40% helix, 21% strand | O66496 |
| D, E, H, L | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 256 | 42% helix, 22% strand | O66496 |
| F | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 255 | 38% helix, 21% strand | O66496 |
| G | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 259 | 43% helix, 19% strand | O66496 |
| I, J | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 262 | 41% helix, 21% strand | O66496 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 17 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C, D, E, F, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.81 | 0.96 | 46 | PEP |
| 2 | 168 | 0.80 | 0.96 | 42 | PO4, PEP |
| 3 | 969 | 0.79 | 0.81 | 101 | empty |
| 4 | 323 | 0.76 | 0.88 | 52 | PEP |
| 5 | 1167 | 0.75 | 0.78 | 94 | empty |
Interfaces
24 interfaces between chains.
- I–J · 1890 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1879 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 1875 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1850 Ų buried · 30 hydrogen bonds · protein-protein
- K–L · 1816 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2NXI · 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 2NXI · PDBe 2NXI · UniProt O66496
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