Research workbench
Actin crystal dynamics: structural implications for F-actin nucleation, polymerization and branching mediated by the anti-parallel dimer
Analyse Actin crystal dynamics: structural implications for F-actin nucleation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RFQ
- Type
- protein
- Length
- 722 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, MG
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin, alpha skeletal muscle | protein | 361 | 38% helix, 15% 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
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.76 | 0.96 | 28 | empty |
| 2 | 75 | 0.75 | 0.98 | 27 | empty |
| 3 | 490 | 0.74 | 0.83 | 62 | MG, ATP, LAR |
| 4 | 569 | 0.72 | 0.80 | 60 | empty |
| 5 | 85 | 0.70 | 0.93 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 548 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1RFQ · Actin Crystal Dynamics: Structural Implications for F-actin Nucleation, Polymerization… · 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 B against A, TM-score 0.97
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 1RFQ · PDBe 1RFQ · UniProt P68135
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