Research workbench
Crystal structure of organophosphate ANHYDROLASE/PROLIDASE mutant Y212F
Analyse Crystal structure of organophosphate ANHYDROLASE/PROLIDASE mutant Y212F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZWO
- Type
- protein
- Length
- 859 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Organophosphate ANHYDROLASE/PROLIDASE
- EC
- 3.4.13.9
- UniProt
- Q44238
- Ligands
- GOA, MN
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Organophosphate ANHYDROLASE/PROLIDASE (EC 3.4.13.9) | protein | 425 | 40% helix, 17% strand | Q44238 |
| B | Organophosphate ANHYDROLASE/PROLIDASE (EC 3.4.13.9) | protein | 434 | 39% helix, 17% strand | Q44238 |
Ligands and binding sites
- GOA · Glycolic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 7 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.85 | 0.86 | 137 | GOA |
| 2 | 81 | 0.38 | 0.77 | 17 | empty |
| 3 | 106 | 0.37 | 0.74 | 17 | empty |
| 4 | 74 | 0.35 | 0.76 | 15 | empty |
| 5 | 57 | 0.32 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2386 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4ZWO · Crystal structure of organophosphate anhydrolase/prolidase mutant Y212F · the same entry in another collection · chain A against A, TM-score 1.00
- Q44238 · AlphaFold monomer V2.0 prediction for xaa-pro dipeptidase (Q44238) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q44238
- Elsewhere: RCSB PDB 4ZWO · PDBe 4ZWO · UniProt Q44238
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