Research workbench
Crystal structure of partial apo (92-227) of cgmp-dependent protein kinase
Analyse Crystal structure of partial apo (92-227) of cgmp-dependent protein kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OGJ
- Type
- protein
- Length
- 509 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PRKG1 protein
- EC
- 2.7.11.12
- UniProt
- Q6P5T7
- Ligands
- CMP, PO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PRKG1 protein (EC 2.7.11.12) | protein | 128 | 30% helix, 32% strand | Q6P5T7 |
| B, C, D | PRKG1 protein (EC 2.7.11.12) | protein | 127 | 30% helix, 31% strand | Q6P5T7 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.84 | 0.85 | 75 | empty |
| 2 | 210 | 0.59 | 0.81 | 42 | empty |
| 3 | 124 | 0.53 | 0.81 | 21 | PO4 |
| 4 | 105 | 0.51 | 0.82 | 20 | CMP |
| 5 | 95 | 0.51 | 0.83 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1015 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 970 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 354 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 354 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 139 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3OGJ · Crystal structure of partial apo (92-227) of cGMP-dependent protein kinase · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6P5T7
- Elsewhere: RCSB PDB 3OGJ · PDBe 3OGJ · UniProt Q6P5T7
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