MolNFT v1 · #114991 · protein
Pkg II'S amino terminal cyclic nucleotide binding domain (cnb-a) in a complex with camp
5C6C · Cgmp-dependent protein kinase 2: “Pkg II'S amino terminal cyclic nucleotide binding domain (cnb-a) in a complex with camp”. X-ray diffraction, 5 ligands (CMP, CD, CO), 1 pocket (best druggability 0.75). MolNFT v1 #114991 on…
- PDB
- 5C6C
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent protein kinase 2
- EC
- 2.7.11.12
- UniProt
- Q13237
- Ligands
- CMP, CD, CO, CA, NA
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent protein kinase 2 (EC 2.7.11.12) | protein | 119 | 29% helix, 33% strand | Q13237 |
| B | Cgmp-dependent protein kinase 2 (EC 2.7.11.12) | protein | 119 | 30% helix, 29% strand | Q13237 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 6 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.75 | 0.81 | 65 | CMP, CA, NA |
Interfaces
1 interface between chains.
- A–B · 367 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5C6C · PKG II's Amino Terminal Cyclic Nucleotide Binding Domain (CNB-A) in a complex with cAMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q13237 · AlphaFold monomer V2.0 prediction for cgmp-dependent protein kinase 2 (Q13237) · 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 Q13237
- Elsewhere: RCSB PDB 5C6C · PDBe 5C6C · UniProt Q13237
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