MolNFT v1 · #72908 · protein
Crystal structure of the leucine zipper domain of cgmp dependent protein kinase I beta
3NMD: “Crystal structure of the leucine zipper domain of cgmp dependent protein kinase I beta”. X-ray diffraction, 4 pockets (best druggability 0.52). MolNFT v1 #72908 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NMD
- Type
- protein
- Length
- 254 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp dependent protein kinase
- UniProt
- Q6P5T7
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 5 distinct chains · 93% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cgmp dependent protein kinase | protein | 53 | 87% helix, 0% strand | Q6P5T7 |
| B | Cgmp dependent protein kinase | protein | 47 | 96% helix, 0% strand | Q6P5T7 |
| C | Cgmp dependent protein kinase | protein | 53 | 92% helix, 0% strand | Q6P5T7 |
| D | Cgmp dependent protein kinase | protein | 50 | 92% helix, 0% strand | Q6P5T7 |
| E | Cgmp dependent protein kinase | protein | 51 | 96% helix, 0% strand | Q6P5T7 |
Ligands and binding sites
- HEZ · Hexane-1,6-diol · additive · 7 copies · chains A, C, D, E
- GOL · Glycerol · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.52 | 0.80 | 18 | empty |
| 2 | 93 | 0.39 | 0.76 | 16 | empty |
| 3 | 53 | 0.30 | 0.76 | 13 | empty |
| 4 | 54 | 0.25 | 0.73 | 13 | HEZ, GOL |
Interfaces
7 interfaces between chains.
- C–D · 1391 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1382 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 725 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 334 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 265 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 3NMD · Crystal structure of the leucine zipper domain of cGMP dependent protein kinase I beta · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6P5T7
- Elsewhere: RCSB PDB 3NMD · PDBe 3NMD · UniProt Q6P5T7
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