Research workbench
Crystal of phnz bound to (R)-2-amino-1-hydroxyethylphosphonic acid
Analyse Crystal of phnz bound to (R)-2-amino-1-hydroxyethylphosphonic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MLN
- Type
- protein
- Length
- 364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted hd phosphohydrolase phnz
- UniProt
- D0E8I5
- Ligands
- ODV, FE
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Predicted hd phosphohydrolase phnz | protein | 182 | 64% helix, 0% strand | D0E8I5 |
| B | Predicted hd phosphohydrolase phnz | protein | 182 | 69% helix, 1% strand | D0E8I5 |
Ligands and binding sites
- ODV · [(1R)-2-amino-1-hydroxyethyl]phosphonic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.72 | 0.94 | 31 | FE, ODV |
| 2 | 51 | 0.54 | 0.89 | 22 | ODV |
| 3 | 185 | 0.42 | 0.72 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 206 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4MLN · Crystal of PhnZ bound to (R)-2-amino-1-hydroxyethylphosphonic acid · the same entry in another collection · chain A against A, TM-score 1.00
- D0E8I5 · AlphaFold monomer V2.0 prediction for 2-amino-1-hydroxyethylphosphonate dioxygenase… · 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 D0E8I5
- Elsewhere: RCSB PDB 4MLN · PDBe 4MLN · UniProt D0E8I5
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