Research workbench
Crystal structure of Toxoplasma gondii micronemal protein 1 bound to 2F-3'SiaLacNAc
Analyse Crystal structure of Toxoplasma gondii micronemal protein 1 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F53
- Type
- protein
- Length
- 231 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Toxoplasma gondii
- Molecule
- Micronemal protein 1
- UniProt
- O00834
- Ligands
- 2FG, SIA, CL
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Micronemal protein 1 | protein | 231 | 31% helix, 33% strand | O00834 |
Ligands and binding sites
- 2FG · 2-deoxy-2-fluoro-beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 8 copies · chains A
- GOL · Glycerol · additive · 5 copies · 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 | 54 | 0.70 | 0.98 | 22 | CL, GOL |
| 2 | 85 | 0.33 | 0.74 | 25 | ACT |
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, engineered).
Compared structures
- 3F53 · Crystal structure of toxoplasma gondii micronemal protein 1 bound to 2F-3'SIALACNAC · the same entry in another collection · chain A against A, TM-score 1.00
- O00834 · AlphaFold monomer V2.0 prediction for micronemal protein 1 (O00834) · 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 O00834
- Elsewhere: RCSB PDB 3F53 · PDBe 3F53 · UniProt O00834
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