Research workbench
Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from bruciella melitensis at 1.85A resolution
Analyse Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from bruciella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FS2
- Type
- protein
- Length
- 507 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
- Q8YHF1
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 258 | 43% helix, 20% strand | Q8YHF1 |
| B | 2-dehydro-3-deoxyphosphooctonate aldolase (EC 2.5.1.55) | protein | 249 | 45% helix, 22% strand | Q8YHF1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.73 | 0.83 | 43 | PO4 |
| 2 | 218 | 0.57 | 0.79 | 24 | empty |
| 3 | 240 | 0.56 | 0.78 | 34 | PO4 |
Interfaces
1 interface between chains.
- A–B · 961 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3FS2 · Crystal structure of 2-Dehydro-3-Deoxyphosphooctonate aldolase from Bruciella melitensis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8YHF1 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxyphosphooctonate aldolase (Q8YHF1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8YHF1
- Elsewhere: RCSB PDB 3FS2 · PDBe 3FS2 · UniProt Q8YHF1
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