Research workbench
Crystal structure of C11N mutant of KDO8P synthase in complex with pep
Analyse Crystal structure of C11N mutant of KDO8P synthase in complex with pep in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NWR
- Type
- protein
- Length
- 512 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, PO4
- Pockets
- 5 · best druggability 0.74
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 | 257 | 42% helix, 20% 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 · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 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 | 291 | 0.74 | 0.87 | 51 | PO4, PEP |
| 2 | 277 | 0.71 | 0.85 | 42 | PO4, PEP |
| 3 | 76 | 0.59 | 0.89 | 29 | empty |
| 4 | 114 | 0.42 | 0.77 | 19 | empty |
| 5 | 52 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1858 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2NWR · Crystal structure of C11N mutant of KDO8P Synthase in complex with PEP · 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 2NWR · PDBe 2NWR · UniProt O66496
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