Research workbench
Pkg II'S carboxyl terminal cyclic nucleotide binding domain (cnb-B) in a complex with cgmp
Analyse Pkg II'S carboxyl terminal cyclic nucleotide binding domain (cnb-B) in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BV6
- Type
- protein
- Length
- 150 residues
- Chains
- 1
- 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
- 35G, CA, NA
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent protein kinase 2 (EC 2.7.11.12) | protein | 150 | 40% helix, 27% strand | Q13237 |
Ligands and binding sites
- 35G · Guanosine-3',5'-monophosphate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · 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 | 117 | 0.72 | 0.93 | 22 | 35G |
Compared structures
- 5BV6 · PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with cGMP · 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 0.81
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 5BV6 · PDBe 5BV6 · UniProt Q13237
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