MolNFT v1 · #4149 · protein
Crystal structure of a DICTYOSTELIUM/TETRAHYMENA chimera actin (mutant 646: Q228K/T229A/A230Y/A231K/S232E/E360H) in complex with human gelsolin segment 1
1DEJ: “Crystal structure of a DICTYOSTELIUM/TETRAHYMENA chimera actin (mutant 646…”. X-ray diffraction, 2 ligands (ATP, CA), 6 pockets (best druggability 0.74). MolNFT v1 #4149 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1DEJ
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gelsolin; Chimeric actin
- UniProt
- P06396, P07830
- Ligands
- ATP, CA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| S | Gelsolin | protein | 127 | 24% helix, 34% strand | P06396 |
| A | Chimeric actin | protein | 368 | 45% helix, 20% strand | P07830 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains S, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.74 | 0.84 | 53 | CA, ATP |
| 2 | 242 | 0.68 | 0.84 | 34 | empty |
| 3 | 193 | 0.46 | 0.75 | 20 | empty |
| 4 | 81 | 0.40 | 0.78 | 17 | empty |
| 5 | 61 | 0.31 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- S–A · 1257 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 1DEJ · Crystal structure of a DICTYOSTELIUM/TETRAHYMENA chimera actin (mutant 646… · 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 A 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 0.94
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 1DEJ · PDBe 1DEJ · UniProt P06396 · UniProt P07830
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