Research workbench
Plasmodium falciparum ATG8 in complex with plasmodium falciparum ATG3 peptide
Analyse Plasmodium falciparum ATG8 in complex with plasmodium falciparum ATG3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EOY
- Type
- protein
- Length
- 394 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Microtubule-associated protein 1 light chain 3; Autophagy-related protein 3
- UniProt
- Q8IJK2, C0H519
- Ligands
- CA, MG, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Microtubule-associated protein 1 light chain 3 | protein | 124 | 31% helix, 26% strand | Q8IJK2 |
| B, C | Microtubule-associated protein 1 light chain 3 | protein | 123 | 32% helix, 26% strand | Q8IJK2 |
| D, E, F | Autophagy-related protein 3 | protein | 8 | 0% helix, 13% strand | C0H519 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, C
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · 3 copies · chains A, F
- ACT · Acetate ion · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.74 | 0.80 | 52 | empty |
| 2 | 484 | 0.67 | 0.78 | 60 | ACT |
| 3 | 50 | 0.29 | 0.76 | 15 | ACT |
| 4 | 71 | 0.29 | 0.73 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–F · 592 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 573 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 549 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 406 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 178 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4EOY · Plasmodium falciparum Atg8 in complex with Plasmodium falciparum Atg3 peptide · 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 Q8IJK2
- Every structure of UniProt C0H519
- Elsewhere: RCSB PDB 4EOY · PDBe 4EOY · UniProt Q8IJK2 · UniProt C0H519
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