Research workbench
CryoEM structure of HSP90-CDC37-BRAF(V600E)-PP5(open) complex
Analyse CryoEM structure of HSP90-CDC37-BRAF(V600E)-PP5(open) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZR6
- Type
- protein
- Length
- 2,168 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.2
- Source
- Homo sapiens
- Molecule
- Heat shock protein HSP 90-beta; Hsp90 co-chaperone Cdc37; Serine/threonine-protein kinase…
- EC
- 2.7.11.1, 3.1.3.16
- UniProt
- P08238, Q16543, P15056, P53041
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 4.2 · 5 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock protein HSP 90-beta | protein | 633 | 34% helix, 17% strand | P08238 |
| B | Heat shock protein HSP 90-beta | protein | 631 | 34% helix, 16% strand | P08238 |
| C | Hsp90 co-chaperone Cdc37 | protein | 277 | 73% helix, 3% strand | Q16543 |
| K | Serine/threonine-protein kinase B-raf (EC 2.7.11.1) | protein | 186 | 40% helix, 4% strand | P15056 |
| P | Serine/threonine-protein phosphatase 5 (EC 3.1.3.16) | protein | 441 | 47% helix, 10% strand | P53041 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.87 | 0.88 | 130 | empty |
| 2 | 790 | 0.83 | 0.86 | 75 | ATP |
| 3 | 518 | 0.83 | 0.89 | 63 | empty |
| 4 | 694 | 0.82 | 0.85 | 67 | ATP |
| 5 | 697 | 0.81 | 0.85 | 67 | empty |
Interfaces
9 interfaces between chains.
- A–B · 3613 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1902 Ų buried · 22 hydrogen bonds · protein-protein
- C–K · 733 Ų buried · 9 hydrogen bonds · protein-protein
- B–K · 438 Ų buried · 3 hydrogen bonds · protein-protein
- A–K · 426 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
- 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 0.92
- P15056 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase B-RAF (P15056) · a predicted model of the same protein · chain K against A, TM-score 0.78
- P53041 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 5 (P53041) · a predicted model of the same protein · chain P 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 C against A, TM-score 0.45
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 P15056
- Every structure of UniProt P53041
- Elsewhere: RCSB PDB 7ZR6 · PDBe 7ZR6 · UniProt P08238 · UniProt Q16543 · UniProt P15056 · UniProt P53041
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