Research workbench
Atomic cryoem structure of HSP90-CDC37-CDK4 complex
Analyse Atomic cryoem structure of HSP90-CDC37-CDK4 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FWL
- Type
- protein
- Length
- 1,818 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock protein HSP 90 beta; HSP90 co-chaperone CDC37; Cyclin-dependent kinase 4
- UniProt
- P08238, Q16543, P11802
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock protein HSP 90 beta | protein | 638 | 40% helix, 19% strand | P08238 |
| B | Heat shock protein HSP 90 beta | protein | 630 | 41% helix, 21% strand | P08238 |
| E | HSP90 co-chaperone CDC37 | protein | 259 | 72% helix, 5% strand | Q16543 |
| K | Cyclin-dependent kinase 4 | protein | 291 | 34% helix, 11% strand | P11802 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.83 | 0.91 | 83 | empty |
| 2 | 263 | 0.82 | 0.94 | 41 | ATP |
| 3 | 608 | 0.82 | 0.87 | 88 | empty |
| 4 | 332 | 0.80 | 0.90 | 52 | ATP, MG |
| 5 | 442 | 0.79 | 0.87 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4139 Ų buried · 50 hydrogen bonds · protein-protein
- B–E · 2102 Ų buried · 39 hydrogen bonds · protein-protein
- A–K · 1634 Ų buried · 30 hydrogen bonds · protein-protein
- B–K · 1306 Ų buried · 22 hydrogen bonds · protein-protein
- E–K · 1065 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5FWL · Atomic cryoEM structure of Hsp90-Cdc37-Cdk4 complex · the same entry in another collection · chain K against K, TM-score 1.00
- P08238 · AlphaFold monomer V2.0 prediction for heat shock protein HSP 90-beta (P08238) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P11802 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 4 (P11802) · a predicted model of the same protein · chain K against A, TM-score 0.63
- Q16543 · AlphaFold monomer V2.0 prediction for HSP90 co-chaperone CDC37 (Q16543) · a predicted model of the same protein · chain E against A, TM-score 0.48
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 P08238
- Every structure of UniProt Q16543
- Every structure of UniProt P11802
- Elsewhere: RCSB PDB 5FWL · PDBe 5FWL · UniProt P08238 · UniProt Q16543 · UniProt P11802
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