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Crystal structure of toxoplasma gondii sporozoite AMA1
Analyse Crystal structure of toxoplasma gondii sporozoite AMA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZLE
- Type
- protein
- Length
- 4,555 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apical membrane antigen 1
- UniProt
- B6K9M7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 14% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Apical membrane antigen 1 | protein | 382 | 14% helix, 29% strand | B6K9M7 |
| B, C, J | Apical membrane antigen 1 | protein | 379 | 15% helix, 28% strand | B6K9M7 |
| D | Apical membrane antigen 1 | protein | 380 | 14% helix, 28% strand | B6K9M7 |
| F | Apical membrane antigen 1 | protein | 377 | 14% helix, 25% strand | B6K9M7 |
| H, K, L | Apical membrane antigen 1 | protein | 380 | 14% helix, 26% strand | B6K9M7 |
| I | Apical membrane antigen 1 | protein | 375 | 14% helix, 30% strand | B6K9M7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, E, F, G, H, K, L
- GOL · Glycerol · additive · 18 copies · chains A, B, C, D, E, G, F, J, H, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1155 | 0.86 | 0.87 | 123 | GOL |
| 2 | 1112 | 0.86 | 0.87 | 116 | GOL |
| 3 | 1084 | 0.84 | 0.85 | 101 | empty |
| 4 | 896 | 0.83 | 0.85 | 68 | empty |
| 5 | 877 | 0.82 | 0.85 | 66 | GOL |
Interfaces
21 interfaces between chains.
- E–G · 949 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 943 Ų buried · 16 hydrogen bonds · protein-protein
- F–J · 933 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 923 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 921 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 96 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 3ZLE · Crystal structure of Toxoplasma gondii sporozoite AMA1 · the same entry in another collection · chain L against L, 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 B6K9M7
- Elsewhere: RCSB PDB 3ZLE · PDBe 3ZLE · UniProt B6K9M7
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