Research workbench
Crystal structure of the adenylate sensor from AMP-activated protein kinase in complex with ADP and ATP
Analyse Crystal structure of the adenylate sensor from AMP-activated protein kinase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QRD
- Type
- protein
- Length
- 1,060 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SNF1-like protein kinase SSP2; SPCC1919.03C protein; Protein C1556.08C
- EC
- 2.7.11.1
- UniProt
- O74536, P78789, Q10343
- Ligands
- ATP, ADP
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SNF1-like protein kinase SSP2 (EC 2.7.11.1) | protein | 114 | 33% helix, 38% strand | O74536 |
| B | SPCC1919.03C protein | protein | 91 | 18% helix, 27% strand | P78789 |
| G | Protein C1556.08C | protein | 325 | 44% helix, 22% strand | Q10343 |
| C | SNF1-like protein kinase SSP2 (EC 2.7.11.1) | protein | 114 | 32% helix, 36% strand | O74536 |
| D | SPCC1919.03C protein | protein | 92 | 18% helix, 25% strand | P78789 |
| E | Protein C1556.08C | protein | 324 | 44% helix, 22% strand | Q10343 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains G, E
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, G, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.83 | 0.84 | 89 | ADP, ATP |
| 2 | 1002 | 0.82 | 0.83 | 92 | ADP, ATP |
| 3 | 169 | 0.70 | 0.89 | 34 | empty |
| 4 | 53 | 0.70 | 0.97 | 17 | empty |
| 5 | 443 | 0.70 | 0.81 | 57 | empty |
Interfaces
11 interfaces between chains.
- C–D · 2441 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2339 Ų buried · 20 hydrogen bonds · protein-protein
- B–G · 1435 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 1404 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 643 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2QRD · Crystal Structure of the Adenylate Sensor from AMP-activated Protein Kinase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q10343 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma… · a predicted model of the same protein · chain E against A, TM-score 0.99
- O74536 · AlphaFold monomer V2.0 prediction for SNF1-like protein kinase SSP2 (O74536) · a predicted model of the same protein · chain C against A, TM-score 0.92
- P78789 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.82
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 O74536
- Every structure of UniProt P78789
- Every structure of UniProt Q10343
- Elsewhere: RCSB PDB 2QRD · PDBe 2QRD · UniProt O74536 · UniProt P78789 · UniProt Q10343
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