Research workbench
Crystal structure of KDO8P synthase in its binary complex with substrate analog 1-deoxy-A5P
Analyse Crystal structure of KDO8P synthase in its binary complex with substrate analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PHW
- Type
- protein
- Length
- 272 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphooctonate aldolase
- EC
- 2.5.1.55
- UniProt
- P0A715
- Ligands
- N
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 272 | 40% helix, 18% strand | P0A715 |
Ligands and binding sites
- N · Any 5'-monophosphate nucleotide · 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 | 461 | 0.71 | 0.81 | 47 | N |
| 2 | 57 | 0.27 | 0.74 | 11 | empty |
Compared structures
- 1PHW · Crystal structure of KDO8P synthase in its binary complex with substrate analog… · 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 0.97
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 1PHW · PDBe 1PHW · UniProt P0A715
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