MolNFT v1 · #97945 · protein
Structures of pkgi reveal a cgmp-selective activation mechanism
4KU8 · Cgmp-dependent protein kinase 1: “Structures of pkgi reveal a cgmp-selective activation mechanism”. X-ray diffraction, 1 ligand (GLY), 8 pockets (best druggability 0.45). MolNFT v1 #97945 on GenesisL1: 3D structure, binding sites…
- PDB
- 4KU8
- Type
- protein
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent protein kinase 1
- UniProt
- Q13976
- Ligands
- GLY
- Pockets
- 8 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent protein kinase 1 | protein | 150 | 37% helix, 26% strand | Q13976 |
| B | Cgmp-dependent protein kinase 1 | protein | 108 | 13% helix, 40% strand | Q13976 |
| C | Cgmp-dependent protein kinase 1 | protein | 122 | 32% helix, 30% strand | Q13976 |
Ligands and binding sites
- GLY · Glycine · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.45 | 0.79 | 18 | empty |
| 2 | 111 | 0.43 | 0.77 | 19 | empty |
| 3 | 98 | 0.41 | 0.77 | 18 | empty |
| 4 | 107 | 0.41 | 0.76 | 17 | GLY |
| 5 | 73 | 0.40 | 0.79 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–C · 420 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 396 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4KU8 · Structures of PKGI Reveal a cGMP-Selective Activation Mechanism · the same entry in another collection · chain C against C, 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 B against A, TM-score 0.87
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 4KU8 · PDBe 4KU8 · UniProt Q13976
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