Research workbench
Polylysine induces an antiparallel actin dimer that nucleates filament assembly: crystal structure at 3.5 a resolution
Analyse Polylysine induces an antiparallel actin dimer that nucleates filament… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LCU
- Type
- protein
- Length
- 732 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ATP, LAR, CA, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 361 | 40% helix, 19% strand | P68135 |
| B | Actin, alpha skeletal muscle | protein | 371 | 39% helix, 18% strand | P68135 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- LAR · Latrunculin A · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.75 | 0.84 | 56 | CA, ATP, LAR |
| 2 | 454 | 0.75 | 0.84 | 55 | CA, ATP, LAR |
| 3 | 613 | 0.67 | 0.76 | 57 | empty |
| 4 | 352 | 0.63 | 0.79 | 40 | CA |
Interfaces
1 interface between chains.
- A–B · 736 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1LCU · Polylysine Induces an Antiparallel Actin Dimer that Nucleates Filament Assembly: Crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 1LCU · PDBe 1LCU · UniProt P68135
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