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Structure of the PHO85-PHO80 cdk-cyclin complex of the phosphate- responsive signal transduction pathway with bound ATP-gamma-S
Analyse Structure of the PHO85-PHO80 cdk-cyclin complex of the phosphate- responsive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PMI
- Type
- protein
- Length
- 998 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent protein kinase PHO85; PHO85 cyclin PHO80
- EC
- 2.7.11.22
- UniProt
- P17157, P20052
- Ligands
- AGS
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent protein kinase PHO85 (EC 2.7.11.22) | protein | 284 | 38% helix, 14% strand | P17157 |
| B | PHO85 cyclin PHO80 | protein | 213 | 54% helix, 1% strand | P20052 |
| C | Cyclin-dependent protein kinase PHO85 (EC 2.7.11.22) | protein | 285 | 38% helix, 13% strand | P17157 |
| D | PHO85 cyclin PHO80 | protein | 216 | 54% helix, 3% strand | P20052 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.81 | 0.83 | 86 | MES |
| 2 | 811 | 0.80 | 0.83 | 68 | MES |
| 3 | 209 | 0.54 | 0.78 | 27 | AGS |
| 4 | 211 | 0.53 | 0.77 | 26 | empty |
| 5 | 124 | 0.48 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1439 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1396 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 636 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 632 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 430 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2PMI · Structure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-responsive Signal… · the same entry in another collection · chain D against D, TM-score 1.00
- P17157 · AlphaFold monomer V2.0 prediction for cyclin-dependent protein kinase PHO85 (P17157) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P20052 · AlphaFold monomer V2.0 prediction for PHO85 cyclin PHO80 (P20052) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P17157
- Every structure of UniProt P20052
- Elsewhere: RCSB PDB 2PMI · PDBe 2PMI · UniProt P17157 · UniProt P20052
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