Research workbench
Structure of rabbit skeletal muscle actin in complex with a hybrid peptide comprising thymosin BETA4 and the lysine-rich region of cordon-bleu
Analyse Structure of rabbit skeletal muscle actin in complex with a hybrid peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PL8
- Type
- protein
- Length
- 728 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Thymosin beta-4,PROTEIN cordon-BLEU,THYMOSIN beta-4
- UniProt
- P68135, P62328, O75128
- Ligands
- ATP, CA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 357 | 45% helix, 20% strand | P68135 |
| H | Thymosin beta-4,PROTEIN cordon-BLEU,THYMOSIN beta-4 | protein | 26 | 35% helix, 8% strand | P62328, O75128 |
| B | Actin, alpha skeletal muscle | protein | 345 | 46% helix, 20% strand | P68135 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.79 | 0.80 | 72 | empty |
| 2 | 433 | 0.77 | 0.86 | 54 | ATP, CA |
| 3 | 325 | 0.72 | 0.85 | 44 | ATP, CA |
Interfaces
3 interfaces between chains.
- A–B · 1063 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 1030 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 328 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4PL8 · Structure of rabbit skeletal muscle actin in complex with a hybrid peptide comprising… · the same entry in another collection · chain H against H, 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 0.98
- P62328 · AlphaFold monomer V2.0 prediction for thymosin beta-4 (P62328) · a predicted model of the same protein · chain H against A, TM-score 0.58
- O75128 · AlphaFold monomer V2.0 prediction for protein cordon-bleu (O75128) · a predicted model of the same protein · chain H against A, TM-score 0.34
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
- Every structure of UniProt P62328
- Every structure of UniProt O75128
- Elsewhere: RCSB PDB 4PL8 · PDBe 4PL8 · UniProt P68135 · UniProt P62328 · UniProt O75128
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