Research workbench
Structure of the yeast actin-human gelsolin segment 1 complex
Analyse Structure of the yeast actin-human gelsolin segment 1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YAG
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (actin); Protein (gelsolin)
- UniProt
- P60010, P06396
- Ligands
- ATP, MG, CA, SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (actin) | protein | 372 | 43% helix, 20% strand | P60010 |
| G | Protein (gelsolin) | protein | 125 | 23% helix, 34% strand | P06396 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CA · Calcium ion · metal · chains G
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.73 | 0.83 | 52 | MG, ATP |
| 2 | 287 | 0.71 | 0.85 | 35 | empty |
| 3 | 162 | 0.45 | 0.75 | 22 | empty |
| 4 | 68 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–G · 1057 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1YAG · Structure of the yeast actin-human gelsolin segment 1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P60010 · AlphaFold monomer V2.0 prediction for actin (P60010) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · a predicted model of the same protein · chain G against A, TM-score 0.95
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 P60010
- Every structure of UniProt P06396
- Elsewhere: RCSB PDB 1YAG · PDBe 1YAG · UniProt P60010 · UniProt P06396
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