Research workbench
Complex of ATP-actin with the N-terminal actin-binding domain of tropomodulin
Analyse Complex of ATP-actin with the N-terminal actin-binding domain of tropomodulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PKG
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; GELSOLIN,TROPOMODULIN-1 chimera
- UniProt
- P68135, P06396, P28289
- Ligands
- ATP, CA
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 371 | 44% helix, 20% strand | P68135 |
| G | GELSOLIN,TROPOMODULIN-1 chimera | protein | 168 | 26% helix, 26% strand | P06396, P28289 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.75 | 0.85 | 56 | ATP, CA |
| 2 | 240 | 0.68 | 0.84 | 36 | empty |
| 3 | 140 | 0.42 | 0.75 | 20 | empty |
| 4 | 83 | 0.41 | 0.79 | 15 | empty |
| 5 | 122 | 0.41 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–G · 2747 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 4PKG · Complex of ATP-actin With the N-terminal Actin-Binding Domain of Tropomodulin · 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 0.97
- P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · a predicted model of the same protein · chain G against A, TM-score 0.71
- P28289 · AlphaFold monomer V2.0 prediction for tropomodulin-1 (P28289) · a predicted model of the same protein · chain G against A, TM-score 0.26
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 P06396
- Every structure of UniProt P28289
- Elsewhere: RCSB PDB 4PKG · PDBe 4PKG · UniProt P68135 · UniProt P06396 · UniProt P28289
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