Research workbench
Crystal structure of the cgmp-dependent protein kinase pkg from plasmodium vivax - amppnp bound
Analyse Crystal structure of the cgmp-dependent protein kinase pkg from plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DZC
- Type
- protein
- Length
- 816 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent protein kinase, putative
- UniProt
- A5K0N4
- Ligands
- ANP, NA, UNX, CL
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent protein kinase, putative | protein | 816 | 35% helix, 26% strand | A5K0N4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- NA · Sodium ion · metal · chains A
- UNX · Unknown atom or ion · ion · 7 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.73 | 0.78 | 63 | empty |
| 2 | 456 | 0.73 | 0.82 | 55 | ANP, NA |
| 3 | 187 | 0.61 | 0.83 | 21 | empty |
| 4 | 169 | 0.51 | 0.78 | 27 | empty |
| 5 | 154 | 0.50 | 0.78 | 20 | empty |
Compared structures
- 5DZC · Crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium Vivax - AMPPNP… · the same entry in another collection · chain A against A, TM-score 1.00
- A5K0N4 · AlphaFold monomer V2.0 prediction for cgmp-dependent protein kinase (A5K0N4) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 A5K0N4
- Elsewhere: RCSB PDB 5DZC · PDBe 5DZC · UniProt A5K0N4
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