Research workbench
Crystal structure of the complex of DNase I/G-ACTIN/PPP1R15A_582-621
Analyse Crystal structure of the complex of DNase I/G-ACTIN/PPP1R15A_582-621 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NXV
- Type
- protein
- Length
- 1,341 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle, intermediate form; Deoxyribonuclease-1; Protein phosphatase…
- EC
- 3.1.21.1
- UniProt
- P68135, P00639, O75807
- Ligands
- ATP, NAG, CA
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin, alpha skeletal muscle, intermediate form | protein | 373 | 41% helix, 21% strand | P68135 |
| B, F | Deoxyribonuclease-1 (EC 3.1.21.1) | protein | 260 | 29% helix, 28% strand | P00639 |
| C | Protein phosphatase 1 regulatory subunit 15A | protein | 38 | 87% helix, 0% strand | O75807 |
| D | Actin, alpha skeletal muscle, intermediate form | protein | 371 | 42% helix, 21% strand | P68135 |
| E | Protein phosphatase 1 regulatory subunit 15A | protein | 39 | 90% helix, 0% strand | O75807 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, F
- CA · Calcium ion · metal · 6 copies · chains A, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.75 | 0.84 | 49 | ATP, CA |
| 2 | 525 | 0.72 | 0.81 | 58 | ATP, CA |
| 3 | 173 | 0.57 | 0.81 | 21 | empty |
| 4 | 480 | 0.56 | 0.73 | 57 | empty |
| 5 | 186 | 0.54 | 0.79 | 27 | empty |
Interfaces
10 interfaces between chains.
- D–E · 1142 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1080 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 829 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 256 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7NXV · Crystal structure of the complex of DNase I/G-actin/PPP1R15A_582-621 · the same entry in another collection · chain F against F, 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 D against A, TM-score 0.98
- O75807 · AlphaFold monomer V2.0 prediction for protein phosphatase 1 regulatory subunit 15A… · a predicted model of the same protein · chain C against A, TM-score 0.74
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
- Every structure of UniProt O75807
- Elsewhere: RCSB PDB 7NXV · PDBe 7NXV · UniProt P68135 · UniProt P00639 · UniProt O75807
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