Research workbench
Actin-DNase I complex
Analyse Actin-DNase I complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A42
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Deoxyribonuclease-1
- EC
- 3.1.21.1
- UniProt
- P68135, P00639
- Ligands
- ATP, NAG, CA, MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle | protein | 361 | 45% helix, 21% strand | P68135 |
| B | Deoxyribonuclease-1 (EC 3.1.21.1) | protein | 255 | 29% helix, 29% strand | P00639 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.73 | 0.84 | 52 | CA, ATP |
| 2 | 83 | 0.36 | 0.76 | 17 | empty |
| 3 | 77 | 0.30 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 899 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, methylation).
Compared structures
- 2A42 · Actin-DNAse I Complex · the same entry in another collection · chain A against A, TM-score 1.00
- P00639 · AlphaFold monomer V2.0 prediction for deoxyribonuclease-1 (P00639) · a predicted model of the same protein · chain B 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
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 P00639
- Elsewhere: RCSB PDB 2A42 · PDBe 2A42 · UniProt P68135 · UniProt P00639
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