Research workbench
Crystal structure of cgmp-dependent protein kinase reveals novel site of interchain communication
Analyse Crystal structure of cgmp-dependent protein kinase reveals novel site of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SHR
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent protein kinase 1
- EC
- 2.7.11.12
- UniProt
- P00516
- Ligands
- CMP, SO4
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cgmp-dependent protein kinase 1 (EC 2.7.11.12) | protein | 278 | 34% helix, 30% strand | P00516 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.50 | 0.80 | 18 | empty |
| 2 | 87 | 0.48 | 0.82 | 18 | empty |
| 3 | 90 | 0.48 | 0.81 | 15 | CMP |
| 4 | 139 | 0.47 | 0.77 | 23 | CMP |
| 5 | 55 | 0.27 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1428 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3SHR · Crystal Structure of cGMP-dependent Protein Kinase Reveals Novel Site of Interchain… · the same entry in another collection · chain A against A, TM-score 1.00
- P00516 · AlphaFold monomer V2.0 prediction for cgmp-dependent protein kinase 1 (P00516) · a predicted model of the same protein · chain A against A, TM-score 0.64
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 P00516
- Elsewhere: RCSB PDB 3SHR · PDBe 3SHR · UniProt P00516
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