Research workbench
X-ray crystal structure of AMP-activated protein kinase alpha-2/ALPHA- 1 rim chimaera (alpha-2(1-347)/ALPHA-1(349-401)/ALPHA-2(397-end) beta-1 gamma-1) co-crystallized with C2 (5-(5-hydroxyl-isoxazol-3- yl)-furan-2-phosphonic acid)
Analyse X-ray crystal structure of AMP-activated protein kinase alpha-2/ALPHA- 1 rim… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EZV
- Type
- protein
- Length
- 1,856 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-AMP-activated protein kinase catalytic subunit alpha- 2/ALPHA-1 rim swap chimera…
- EC
- 2.7.11.1, 2.7.11.27, 2.7.11.31
- UniProt
- P54646, Q13131, Q9Y478, P54619
- Ligands
- C2Z, STU, C1V
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-AMP-activated protein kinase catalytic subunit alpha- 2/ALPHA-1 rim swap chimera (EC 2.7.11.1, 2.7.11.27, 2.7.11.31) | protein | 442 | 40% helix, 19% strand | P54646, Q13131 |
| B | 5'-AMP-activated protein kinase subunit beta-1 | protein | 185 | 11% helix, 38% strand | Q9Y478 |
| C | 5'-AMP-activated protein kinase catalytic subunit alpha- 2/ALPHA-1 rim swap chimera (EC 2.7.11.1, 2.7.11.27, 2.7.11.31) | protein | 441 | 37% helix, 20% strand | P54646, Q13131 |
| D | 5'-AMP-activated protein kinase subunit beta-1 | protein | 186 | 16% helix, 39% strand | Q9Y478 |
| E | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 302 | 38% helix, 22% strand | P54619 |
| F | 5'-AMP-activated protein kinase subunit gamma-1 | protein | 300 | 40% helix, 22% strand | P54619 |
Ligands and binding sites
- C2Z · 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid · ligand · 4 copies · chains E, F
- STU · Staurosporine · ligand · 2 copies · chains A, C
- C1V · 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.81 | 0.84 | 76 | C2Z |
| 2 | 952 | 0.80 | 0.82 | 84 | C2Z |
| 3 | 1122 | 0.73 | 0.76 | 75 | empty |
| 4 | 1108 | 0.72 | 0.76 | 69 | empty |
| 5 | 206 | 0.69 | 0.87 | 35 | empty |
Interfaces
7 interfaces between chains.
- C–D · 4156 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 4037 Ų buried · 51 hydrogen bonds · protein-protein
- C–F · 1392 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 1352 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1285 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 5EZV · X-ray crystal structure of AMP-activated protein kinase alpha-2/alpha-1 RIM chimaera… · the same entry in another collection · chain B against B, TM-score 1.00
- Q13131 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P54619 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma-1… · a predicted model of the same protein · chain F against A, TM-score 0.96
- P54646 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P54646
- Every structure of UniProt Q13131
- Every structure of UniProt Q9Y478
- Every structure of UniProt P54619
- Elsewhere: RCSB PDB 5EZV · PDBe 5EZV · UniProt P54646 · UniProt Q13131 · UniProt Q9Y478 · UniProt P54619
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