MolNFT v1 · #181443 · protein
Crystal structure of human protein kinase G (pkg) R-C complex in inhibited state
7LV3 · Isoform beta of cgmp-dependent protein kinase 1: “Crystal structure of human protein kinase G (pkg) R-C complex in inhibited state”. X-ray diffraction, 2 ligands (ANP, MN), 17 pockets (best druggability 0.80). MolNFT v1 #181443 on…
- PDB
- 7LV3
- Type
- protein
- Length
- 1,195 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform beta of cgmp-dependent protein kinase 1
- EC
- 2.7.11.12
- UniProt
- Q13976
- Ligands
- ANP, MN
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform beta of cgmp-dependent protein kinase 1 (EC 2.7.11.12) | protein | 601 | 34% helix, 23% strand | Q13976 |
| B | Isoform beta of cgmp-dependent protein kinase 1 (EC 2.7.11.12) | protein | 594 | 31% helix, 24% strand | Q13976 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.80 | 0.91 | 41 | MN, ANP |
| 2 | 797 | 0.77 | 0.81 | 83 | MN, ANP |
| 3 | 489 | 0.69 | 0.80 | 64 | empty |
| 4 | 409 | 0.65 | 0.79 | 50 | empty |
| 5 | 268 | 0.57 | 0.77 | 27 | EDO |
Interfaces
1 interface between chains.
- A–B · 3500 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7LV3 · Crystal structure of human protein kinase G (PKG) R-C complex in inhibited state · 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 B against A, TM-score 0.55
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 7LV3 · PDBe 7LV3 · UniProt Q13976
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