MolNFT v1 · #55072 · protein
Crystal structure of apo AMA1 mutant (TYR230ALA) from toxoplasma gondii
2Y8R · Apical membrane antigen, putative: “Crystal structure of apo AMA1 mutant (TYR230ALA) from toxoplasma gondii”. X-ray diffraction, 1 ligand (NAG), 19 pockets (best druggability 0.84). MolNFT v1 #55072 on GenesisL1: 3D structure…
- PDB
- 2Y8R
- Type
- protein
- Length
- 1,596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apical membrane antigen, putative
- UniProt
- B9QC59
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apical membrane antigen, putative | protein | 399 | 15% helix, 28% strand | B9QC59 |
| B | Apical membrane antigen, putative | protein | 397 | 15% helix, 27% strand | B9QC59 |
| D | Apical membrane antigen, putative | protein | 406 | 15% helix, 27% strand | B9QC59 |
| E | Apical membrane antigen, putative | protein | 394 | 15% helix, 27% strand | B9QC59 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.84 | 0.85 | 120 | empty |
| 2 | 1104 | 0.73 | 0.76 | 88 | empty |
| 3 | 58 | 0.68 | 0.96 | 17 | empty |
| 4 | 290 | 0.67 | 0.82 | 53 | empty |
| 5 | 66 | 0.63 | 0.92 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–E · 733 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 602 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 514 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 391 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 360 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2Y8R · Crystal structure of apo AMA1 mutant (Tyr230Ala) 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
- Elsewhere: RCSB PDB 2Y8R · PDBe 2Y8R · UniProt B9QC59
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