Research workbench
Designed tpr module (CTPR390) in complex with its peptide-ligand (HSP90 peptide)
Analyse Designed tpr module (CTPR390) in complex with its peptide-ligand (HSP90 peptide) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KD7
- Type
- protein
- Length
- 529 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CTPR390; HSP90 meevd peptide
- Ligands
- ACE
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CTPR390 | protein | 102 | 78% helix, 0% strand | — |
| B, E | CTPR390 | protein | 100 | 79% helix, 0% strand | — |
| C, D | CTPR390 | protein | 101 | 80% helix, 0% strand | — |
| G, H, I, J, K | HSP90 meevd peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 5 copies · chains G, H, I, J, C, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.59 | 0.75 | 58 | empty |
| 2 | 130 | 0.49 | 0.79 | 15 | empty |
| 3 | 108 | 0.46 | 0.79 | 23 | empty |
| 4 | 105 | 0.43 | 0.78 | 17 | empty |
| 5 | 142 | 0.38 | 0.73 | 25 | empty |
Interfaces
18 interfaces between chains.
- A–D · 563 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 562 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 525 Ų buried · 4 hydrogen bonds · protein-protein
- D–J · 437 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 437 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 3KD7 · Designed TPR module (CTPR390) in complex with its peptide-ligand (Hsp90 peptide) · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3KD7 · PDBe 3KD7
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