Research workbench
Crystal structures of KDO8P synthase in its binary complex with substrate phosphoenol pyruvate
Analyse Crystal structures of KDO8P synthase in its binary complex with substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G7U
- Type
- protein
- Length
- 284 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 4.1.2.16
- UniProt
- P0A715
- Ligands
- PEP
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 4.1.2.16) | protein | 284 | 37% helix, 16% strand | P0A715 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.70 | 0.82 | 37 | PEP |
| 2 | 78 | 0.29 | 0.73 | 15 | empty |
Compared structures
- 1G7U · Crystal structures of KDO8P synthase in its binary complex with substrate phosphoenol… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A715 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (P0A715) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P0A715
- Elsewhere: RCSB PDB 1G7U · PDBe 1G7U · UniProt P0A715
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