Research workbench
Cryo-EM structure of jasplakinolide-stabilized malaria parasite F- actin at near-atomic resolution
Analyse Cryo-EM structure of jasplakinolide-stabilized malaria parasite F- actin at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OGW
- Type
- protein
- Length
- 1,850 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-1
- UniProt
- P86287
- Ligands
- ADP, 9UE, MG
- Pockets
- 15 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin-1 | protein | 370 | 39% helix, 19% strand | P86287 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
- 9UE · Jasplakinolide · ligand · 3 copies · chains A, B, D, C, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.79 | 0.91 | 52 | ADP, MG |
| 2 | 644 | 0.78 | 0.83 | 75 | empty |
| 3 | 607 | 0.77 | 0.83 | 78 | empty |
| 4 | 282 | 0.76 | 0.89 | 55 | ADP, MG |
| 5 | 267 | 0.76 | 0.89 | 49 | ADP, MG |
Interfaces
7 interfaces between chains.
- D–E · 1206 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1200 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1200 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 521 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 514 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5OGW · Cryo-EM structure of jasplakinolide-stabilized malaria parasite F-actin at near-atomic… · the same entry in another collection · chain E against E, TM-score 1.00
- P86287 · AlphaFold monomer V2.0 prediction for actin-1 (P86287) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 P86287
- Elsewhere: RCSB PDB 5OGW · PDBe 5OGW · UniProt P86287
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