Research workbench
Crystal structure of a transition state mimic of the catalytic subunit of camp-dependent protein kinase
Analyse Crystal structure of a transition state mimic of the catalytic subunit of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L3R
- Type
- protein
- Length
- 361 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase, alpha-catalytic subunit; Camp-dependent protein kinase…
- EC
- 2.7.1.37
- UniProt
- P05132, P27776
- Ligands
- ADP, AF3, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Camp-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) | protein | 341 | 36% helix, 15% strand | P05132 |
| I | Camp-dependent protein kinase inhibitor, MUSCLE/BRAIN form | protein | 20 | 35% helix, 5% strand | P27776 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains E, I
- AF3 · Aluminum fluoride · ligand · chains E, I
- MG · Magnesium ion · metal · 2 copies · chains E, I
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.80 | 0.96 | 33 | MG, ADP, AF3 |
| 2 | 102 | 0.42 | 0.78 | 18 | empty |
| 3 | 85 | 0.40 | 0.77 | 12 | MPD |
| 4 | 76 | 0.33 | 0.75 | 21 | empty |
| 5 | 65 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- E–I · 1151 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 1L3R · Crystal Structure of a Transition State Mimic of the Catalytic Subunit of cAMP-dependent… · the same entry in another collection · chain E against E, 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 P05132
- Every structure of UniProt P27776
- Elsewhere: RCSB PDB 1L3R · PDBe 1L3R · UniProt P05132 · UniProt P27776
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