MolNFT v1 · #55380 · protein
Crystal structure of parasite sarcocystis muris microneme protein sml- 2 in complex with 1-thio-beta-D-galactose (spacegroup C2221)
2YIO · Microneme antigen L2: “Crystal structure of parasite sarcocystis muris microneme protein sml- 2 in complex with…”. X-ray diffraction, 3 ligands (YIO, CL, SO4), 1 pocket (best druggability 0.30). MolNFT v1 #55380 on GenesisL1: 3D…
- PDB
- 2YIO
- Type
- protein
- Length
- 259 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microneme antigen L2
- UniProt
- P81860
- Ligands
- YIO, CL, SO4
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Microneme antigen L2 | protein | 128 | 14% helix, 32% strand | P81860 |
| B | Microneme antigen L2 | protein | 131 | 16% helix, 31% strand | P81860 |
Ligands and binding sites
- YIO · 1-thio-beta-D-galactopyranose · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 9 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 448 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2YIO · Crystal Structure of Parasite Sarcocystis muris Microneme Protein SML- 2 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P81860 · AlphaFold monomer V2.0 prediction for microneme antigen L2 (P81860) · a predicted model of the same protein · chain A against A, TM-score 0.59
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 P81860
- Elsewhere: RCSB PDB 2YIO · PDBe 2YIO · UniProt P81860
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