Research workbench
Structure of the cgmp dependent protein kinase II and RAB11B complex
Analyse Structure of the cgmp dependent protein kinase II and RAB11B complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OJK
- Type
- protein
- Length
- 404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-11B; Cgmp-dependent protein kinase 2
- EC
- 3.6.5.2
- UniProt
- Q15907, Q64595
- Ligands
- GDP
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-11B (EC 3.6.5.2) | protein | 174 | 39% helix, 27% strand | Q15907 |
| B | RAS-related protein rab-11B (EC 3.6.5.2) | protein | 160 | 39% helix, 29% strand | Q15907 |
| C | Cgmp-dependent protein kinase 2 | protein | 37 | 89% helix, 0% strand | Q64595 |
| D | Cgmp-dependent protein kinase 2 | protein | 33 | 85% helix, 0% strand | Q64595 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
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 | 348 | 0.65 | 0.80 | 46 | empty |
| 2 | 127 | 0.43 | 0.76 | 18 | empty |
| 3 | 100 | 0.39 | 0.76 | 22 | GDP |
| 4 | 52 | 0.24 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 827 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 667 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 541 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4OJK · Structure of the cGMP Dependent Protein Kinase II and Rab11b Complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q15907 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-11B (Q15907) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q64595 · AlphaFold monomer V2.0 prediction for cgmp-dependent protein kinase 2 (Q64595) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q15907
- Every structure of UniProt Q64595
- Elsewhere: RCSB PDB 4OJK · PDBe 4OJK · UniProt Q15907 · UniProt Q64595
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