Research workbench
Crystal structure of the adenylate sensor from AMP- activated protein kinase complexed with ATP
Analyse Crystal structure of the adenylate sensor from AMP- activated protein kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OOY
- Type
- protein
- Length
- 1,084 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SNF1-like protein kinase SSP2; SPCC1919.03C protein; Hypothetical protein C1556.08C in…
- EC
- 2.7.11.1
- UniProt
- O74536, P78789, Q10343
- Ligands
- ATP
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SNF1-like protein kinase SSP2 (EC 2.7.11.1) | protein | 129 | 28% helix, 33% strand | O74536 |
| B | SPCC1919.03C protein | protein | 92 | 12% helix, 28% strand | P78789 |
| G | Hypothetical protein C1556.08C in chromosome I | protein | 324 | 39% helix, 21% strand | Q10343 |
| C | SNF1-like protein kinase SSP2 (EC 2.7.11.1) | protein | 115 | 26% helix, 30% strand | O74536 |
| D | SPCC1919.03C protein | protein | 91 | 3% helix, 30% strand | P78789 |
| E | Hypothetical protein C1556.08C in chromosome I | protein | 333 | 40% helix, 20% strand | Q10343 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains G, E
- FLC · Citrate anion · additive · chains 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 | 1078 | 0.83 | 0.84 | 116 | FLC, ATP |
| 2 | 680 | 0.82 | 0.86 | 70 | ATP |
| 3 | 579 | 0.73 | 0.81 | 63 | empty |
| 4 | 229 | 0.71 | 0.87 | 48 | empty |
| 5 | 242 | 0.64 | 0.82 | 53 | empty |
Interfaces
11 interfaces between chains.
- C–D · 2444 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2428 Ų buried · 17 hydrogen bonds · protein-protein
- B–G · 1424 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1401 Ų buried · 23 hydrogen bonds · protein-protein
- A–G · 642 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2OOY · Crystal structure of the adenylate sensor from AMP-activated protein kinase complexed… · the same entry in another collection · chain E against E, 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 G against A, TM-score 0.98
- 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 0.90
- P78789 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit beta… · a predicted model of the same protein · chain D against A, TM-score 0.81
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 2OOY · PDBe 2OOY · UniProt O74536 · UniProt P78789 · UniProt Q10343
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