MolNFT v1 · #41234 · protein
Crystal structure of toxoplasma gondii micronemal protein 1 bound to 3'-sialyl-N-acetyllactosamine
2JHD: “Crystal structure of toxoplasma gondii micronemal protein 1 bound to 3'-sialyl-N-acetyllactosamine”. X-ray diffraction, 3 ligands (GAL, SIA, CL), 2 pockets (best druggability 0.71). MolNFT v1 #41234 on GenesisL1: 3D structure…
- PDB
- 2JHD
- Type
- protein
- Length
- 227 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Micronemal protein 1
- UniProt
- O00834
- Ligands
- GAL, SIA, CL
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Micronemal protein 1 | protein | 227 | 31% helix, 34% strand | O00834 |
Ligands and binding sites
- GAL · 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 · 3 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 | 0.71 | 0.99 | 24 | CL, GOL |
| 2 | 82 | 0.32 | 0.74 | 24 | ACT |
Modifications
Observed in the structure: 7 disulfide, 2 modified (disulfide, engineered).
Compared structures
- 2JHD · Crystal structure of Toxoplasma gondii micronemal protein 1 bound to… · 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 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 O00834
- Elsewhere: RCSB PDB 2JHD · PDBe 2JHD · UniProt O00834
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