Research workbench
Crystal structure of a dictyostelium P109A CA2+-actin in complex with human gelsolin segment 1
Analyse Crystal structure of a dictyostelium P109A CA2+-actin in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A5N
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gelsolin; Major actin
- UniProt
- P06396, P07830
- Ligands
- ATP, CA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Gelsolin | protein | 123 | 24% helix, 33% strand | P06396 |
| C | Major actin | protein | 360 | 45% helix, 21% strand | P07830 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains C
- CA · Calcium ion · metal · 3 copies · chains S, C
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 | 386 | 0.72 | 0.84 | 59 | CA, ATP |
| 2 | 136 | 0.60 | 0.85 | 25 | empty |
| 3 | 180 | 0.47 | 0.76 | 22 | empty |
| 4 | 97 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- S–C · 1023 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 3A5N · Crystal Structure of a Dictyostelium P109A Ca2+-Actin in Complex with Human Gelsolin… · the same entry in another collection · chain S against S, TM-score 1.00
- P07830 · AlphaFold monomer V2.0 prediction for major actin (P07830) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P06396 · AlphaFold monomer V2.0 prediction for gelsolin (P06396) · a predicted model of the same protein · chain S 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 P06396
- Every structure of UniProt P07830
- Elsewhere: RCSB PDB 3A5N · PDBe 3A5N · UniProt P06396 · UniProt P07830
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