Research workbench
Crystal structure of cgmp-dependent protein kinase ialpha (pkg ialpha) catalytic domain bound with N46
Analyse Crystal structure of cgmp-dependent protein kinase ialpha (pkg ialpha)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C0T
- Type
- protein
- Length
- 335 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent protein kinase 1
- EC
- 2.7.11.12
- UniProt
- Q13976
- Ligands
- EE4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent protein kinase 1 (EC 2.7.11.12) | protein | 335 | 39% helix, 16% strand | Q13976 |
Ligands and binding sites
- EE4 · N-[(3R,4R)-4-{[4-(2-fluoro-3-methoxy-6-propoxybenzene-1-carbonyl)benzene-1-carbonyl]amino}pyrrolidin-3-yl]-1H-indazole-5-carboxamide · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- PGE · Triethylene glycol · additive · 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 | 339 | 0.70 | 0.83 | 40 | EE4, DMS |
| 2 | 139 | 0.38 | 0.73 | 25 | PGE |
| 3 | 61 | 0.30 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6C0T · Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13976 · AlphaFold monomer V2.0 prediction for cgmp-dependent protein kinase 1 (Q13976) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q13976
- Elsewhere: RCSB PDB 6C0T · PDBe 6C0T · UniProt Q13976
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.