Research workbench
Co-structure of AMA1 with a surface exposed region of RON2 from toxoplasma gondii
Analyse Co-structure of AMA1 with a surface exposed region of RON2 from toxoplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y8T
- Type
- protein
- Length
- 856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apical membrane antigen, putative; Rhoptry neck protein 2
- UniProt
- B9QC59, B9QQC1
- Ligands
- NAG, BO3
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apical membrane antigen, putative | protein | 388 | 18% helix, 29% strand | B9QC59 |
| B | Rhoptry neck protein 2 | protein | 37 | 19% helix, 24% strand | B9QQC1 |
| D | Apical membrane antigen, putative | protein | 395 | 16% helix, 29% strand | B9QC59 |
| E | Rhoptry neck protein 2 | protein | 36 | 19% helix, 25% strand | B9QQC1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D
- BO3 · Boric acid · ion · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.87 | 0.88 | 133 | empty |
| 2 | 69 | 0.51 | 0.85 | 20 | empty |
| 3 | 153 | 0.44 | 0.75 | 31 | empty |
| 4 | 65 | 0.31 | 0.74 | 15 | empty |
| 5 | 53 | 0.29 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–E · 1949 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1807 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 930 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 2Y8T · Co-structure of AMA1 with a surface exposed region of RON2 from Toxoplasma gondii · the same entry in another collection · 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 B9QC59
- Every structure of UniProt B9QQC1
- Elsewhere: RCSB PDB 2Y8T · PDBe 2Y8T · UniProt B9QC59 · UniProt B9QQC1
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