Research workbench
Crystal structure of actin in complex with swinholide a
Analyse Crystal structure of actin in complex with swinholide a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YXQ
- Type
- protein
- Length
- 715 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ATP, SWI, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 356 | 46% helix, 21% strand | P68135 |
| B | Actin, alpha skeletal muscle | protein | 359 | 46% helix, 21% strand | P68135 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- SWI · Swinholide A · ligand · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.73 | 0.84 | 53 | MG, ATP |
| 2 | 345 | 0.72 | 0.85 | 53 | MG, ATP |
| 3 | 478 | 0.58 | 0.74 | 46 | EDO, SWI |
| 4 | 178 | 0.46 | 0.75 | 32 | empty |
| 5 | 136 | 0.45 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 131 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
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 P68135
- Elsewhere: RCSB PDB 1YXQ · PDBe 1YXQ · UniProt P68135
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