Research workbench
PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma
Analyse PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WJF
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 7.5
- Source
- Homo sapiens; Rattus norvegicus
- Molecule
- DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha…
- EC
- 2.7.11.11
- UniProt
- P25685, P17612, P12369
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 7.5 · 4 distinct chains · 30% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha fusion (EC 2.7.11.11) | protein | 405 | 36% helix, 10% strand | P25685, P17612 |
| B | DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha fusion (EC 2.7.11.11) | protein | 310 | 27% helix, 13% strand | P25685, P17612 |
| C | cAMP-dependent protein kinase type II-beta regulatory subunit | protein | 295 | 24% helix, 15% strand | P12369 |
| D | cAMP-dependent protein kinase type II-beta regulatory subunit | protein | 162 | 28% helix, 22% strand | P12369 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.88 | 0.88 | 143 | empty |
| 2 | 678 | 0.87 | 0.91 | 94 | empty |
| 3 | 1010 | 0.86 | 0.87 | 104 | empty |
| 4 | 688 | 0.85 | 0.88 | 76 | empty |
| 5 | 434 | 0.85 | 0.92 | 64 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1748 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1272 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 647 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 604 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 517 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6WJF · PKA riibeta holoenzyme with DNAJB1-pkac fusion in fibrolamellar hepatoceullar carcinoma · the same entry in another collection · chain A against A, TM-score 1.00
- P17612 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain B against A, TM-score 0.90
- P12369 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase type II-beta… · a predicted model of the same protein · chain D against A, TM-score 0.88
- P25685 · AlphaFold monomer V2.0 prediction for dnaj homolog subfamily B member 1 (P25685) · a predicted model of the same protein · chain B against A, TM-score 0.22
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 P25685
- Every structure of UniProt P17612
- Every structure of UniProt P12369
- Elsewhere: RCSB PDB 6WJF · PDBe 6WJF · UniProt P25685 · UniProt P17612 · UniProt P12369
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