MolNFT v1 · #115080 · protein
Pkg II'S amino terminal cyclic nucleotide binding domain (cnb-a) in a complex with cgmp
5C8W · Cgmp-dependent protein kinase 2: “Pkg II'S amino terminal cyclic nucleotide binding domain (cnb-a) in a complex with cgmp”. X-ray diffraction, 2 ligands (PCG, NA), 7 pockets (best druggability 0.70). MolNFT v1 #115080 on GenesisL1…
- PDB
- 5C8W
- Type
- protein
- Length
- 718 residues
- Chains
- 6
- 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
- PCG, NA
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent protein kinase 2 (EC 2.7.11.12) | protein | 120 | 33% helix, 32% strand | Q13237 |
| B | Cgmp-dependent protein kinase 2 (EC 2.7.11.12) | protein | 121 | 32% helix, 31% strand | Q13237 |
| C | Cgmp-dependent protein kinase 2 (EC 2.7.11.12) | protein | 121 | 32% helix, 33% strand | Q13237 |
| D | Cgmp-dependent protein kinase 2 (EC 2.7.11.12) | protein | 119 | 32% helix, 33% strand | Q13237 |
| E | Cgmp-dependent protein kinase 2 (EC 2.7.11.12) | protein | 119 | 34% helix, 32% strand | Q13237 |
| F | Cgmp-dependent protein kinase 2 (EC 2.7.11.12) | protein | 118 | 32% helix, 32% strand | Q13237 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · 6 copies · chains A, B, C, E, D, F
- NA · Sodium ion · metal · 3 copies · chains A, B, C, E, F
- MLA · Malonic acid · additive · 7 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.70 | 0.82 | 36 | PCG |
| 2 | 305 | 0.69 | 0.83 | 31 | PCG |
| 3 | 273 | 0.68 | 0.84 | 31 | PCG |
| 4 | 274 | 0.66 | 0.82 | 31 | PCG |
| 5 | 274 | 0.53 | 0.75 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–B · 755 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 694 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 558 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 353 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C8W · PKG II's Amino Terminal Cyclic Nucleotide Binding Domain (CNB-A) in a complex with cGMP · the same entry in another collection · chain F against F, 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 F 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 5C8W · PDBe 5C8W · UniProt Q13237
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