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Crystal structure of a L205R mutant of human camp-dependent protein kinase a (catalytic alpha subunit)
Analyse Crystal structure of a L205R mutant of human camp-dependent protein kinase a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WB6
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Pki (5-24)
- EC
- 2.7.11.11
- UniProt
- P17612
- Ligands
- ATP, MG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 338 | 37% helix, 15% strand | P17612 |
| B | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 343 | 39% helix, 15% strand | P17612 |
| I | Pki (5-24) | protein | 19 | 32% helix, 0% strand | — |
| J | Pki (5-24) | protein | 20 | 25% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, I, B, J
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.82 | 0.97 | 34 | ATP, MG |
| 2 | 149 | 0.81 | 0.97 | 32 | ATP, MG |
| 3 | 935 | 0.75 | 0.78 | 53 | empty |
| 4 | 167 | 0.57 | 0.81 | 22 | empty |
| 5 | 81 | 0.46 | 0.80 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–J · 994 Ų buried · 24 hydrogen bonds · protein-protein
- A–I · 945 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 572 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (phosphorylation).
Compared structures
- 4WB6 · Crystal structure of a L205R mutant of human cAMP-dependent protein kinase A (catalytic… · 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 A 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 P17612
- Elsewhere: RCSB PDB 4WB6 · PDBe 4WB6 · UniProt P17612
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