Research workbench
The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase complexed with tungstate, a product analog
Analyse The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FEZ
- Type
- protein
- Length
- 1,024 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphonoacetaldehyde hydrolase
- UniProt
- O31156
- Ligands
- MG, WO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphonoacetaldehyde hydrolase | protein | 256 | 50% helix, 10% strand | O31156 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- WO4 · Tungstate(vi)ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.76 | 0.86 | 37 | MG |
| 2 | 383 | 0.75 | 0.85 | 42 | MG |
| 3 | 84 | 0.35 | 0.75 | 25 | empty |
| 4 | 57 | 0.30 | 0.75 | 14 | empty |
| 5 | 54 | 0.29 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 711 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 701 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1FEZ · The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- O31156 · AlphaFold monomer V2.0 prediction for phosphonoacetaldehyde hydrolase (O31156) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 O31156
- Elsewhere: RCSB PDB 1FEZ · PDBe 1FEZ · UniProt O31156
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