Research workbench
Crystal structure of toxoplasma gondii AMA4 di-dii-EGF1 in complex with a 33 aa TGRON2L1 peptide
Analyse Crystal structure of toxoplasma gondii AMA4 di-dii-EGF1 in complex with a 33 aa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z80
- Type
- protein
- Length
- 995 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EGF family domain-containing protein; Cytoadherence-linked asexual protein
- UniProt
- V4YLU4, B6KQU6
- Ligands
- NAG, SO4
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | EGF family domain-containing protein | protein | 466 | 17% helix, 26% strand | V4YLU4 |
| C | Cytoadherence-linked asexual protein | protein | 32 | 25% helix, 9% strand | B6KQU6 |
| D | Cytoadherence-linked asexual protein | protein | 31 | 26% helix, 10% strand | B6KQU6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.61 | 0.79 | 42 | empty |
| 2 | 88 | 0.48 | 0.82 | 18 | empty |
| 3 | 60 | 0.48 | 0.85 | 15 | empty |
| 4 | 51 | 0.39 | 0.81 | 13 | empty |
| 5 | 103 | 0.36 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1307 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1267 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 468 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4Z80 · Crystal structure of Toxoplasma gondii AMA4 DI-DII-EGF1 in complex with a 33 aa TgRON2L1… · 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 V4YLU4
- Every structure of UniProt B6KQU6
- Elsewhere: RCSB PDB 4Z80 · PDBe 4Z80 · UniProt V4YLU4 · UniProt B6KQU6
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