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Co-crystal structure of the tandem cnb (cnb-A/B) domains of human pkg I beta with cgmp
Analyse Co-crystal structure of the tandem cnb (cnb-A/B) domains of human pkg I beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z07
- Type
- protein
- Length
- 644 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-dependent protein kinase 1
- EC
- 2.7.11.12
- UniProt
- Q13976
- Ligands
- PCG, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp-dependent protein kinase 1 (EC 2.7.11.12) | protein | 260 | 28% helix, 31% strand | Q13976 |
| C | Cgmp-dependent protein kinase 1 (EC 2.7.11.12) | protein | 258 | 29% helix, 30% strand | Q13976 |
| E | Cgmp-dependent protein kinase 1 (EC 2.7.11.12) | protein | 126 | 29% helix, 32% strand | Q13976 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · 5 copies · chains A, C, E
- SO4 · Sulfate ion · ion · chains C
- IPA · Isopropyl alcohol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.76 | 0.83 | 69 | empty |
| 2 | 490 | 0.75 | 0.84 | 44 | PCG |
| 3 | 483 | 0.71 | 0.81 | 46 | PCG |
| 4 | 106 | 0.64 | 0.88 | 18 | PCG |
| 5 | 108 | 0.60 | 0.86 | 23 | PCG |
Interfaces
3 interfaces between chains.
- A–E · 1032 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 944 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Z07 · Co-crystal structure of the tandem CNB (CNB-A/B) domains of human PKG I beta with cGMP · 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 E 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 Q13976
- Elsewhere: RCSB PDB 4Z07 · PDBe 4Z07 · UniProt Q13976
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