Research workbench
First tpr of spaghetti (RPAP3) bound to HSP90 peptide srmeevd
Analyse First tpr of spaghetti (RPAP3) bound to HSP90 peptide srmeevd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CGV
- Type
- protein
- Length
- 511 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase II-associated protein 3; Heat shock protein HSP 90-alpha
- UniProt
- Q9H6T3, P07900
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase II-associated protein 3 | protein | 125 | 78% helix, 0% strand | Q9H6T3 |
| B | RNA polymerase II-associated protein 3 | protein | 126 | 79% helix, 0% strand | Q9H6T3 |
| C | RNA polymerase II-associated protein 3 | protein | 126 | 76% helix, 0% strand | Q9H6T3 |
| D | RNA polymerase II-associated protein 3 | protein | 123 | 80% helix, 0% strand | Q9H6T3 |
| E | Heat shock protein HSP 90-alpha | protein | 7 | 0% helix, 0% strand | P07900 |
| F | Heat shock protein HSP 90-alpha | protein | 4 | 0% helix, 0% strand | P07900 |
Ligands and binding sites
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.68 | 0.76 | 83 | empty |
| 2 | 258 | 0.61 | 0.80 | 37 | empty |
| 3 | 140 | 0.49 | 0.79 | 28 | empty |
| 4 | 54 | 0.32 | 0.77 | 11 | empty |
Interfaces
8 interfaces between chains.
- B–C · 656 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 376 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 357 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 357 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 298 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4CGV · First TPR of Spaghetti (RPAP3) bound to HSP90 peptide SRMEEVD · the same entry in another collection · chain F against F, TM-score 1.00
- Q9H6T3 · AlphaFold monomer V2.0 prediction for RNA polymerase II-associated protein 3 (Q9H6T3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9H6T3
- Every structure of UniProt P07900
- Elsewhere: RCSB PDB 4CGV · PDBe 4CGV · UniProt Q9H6T3 · UniProt P07900
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