Research workbench
Crystal structure of WDR5 in complex with the win peptide of PDPK1
Analyse Crystal structure of WDR5 in complex with the win peptide of PDPK1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WJQ
- Type
- protein
- Length
- 623 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; 3-phosphoinositide-dependent protein kinase 1
- EC
- 2.7.11.1
- UniProt
- P61964, O15530
- Ligands
- ACE
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 300 | 0% helix, 53% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 303 | 0% helix, 52% strand | P61964 |
| C, D | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 10 | 0% helix, 0% strand | O15530 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 864 | 0.83 | 0.85 | 64 | empty |
| 2 | 497 | 0.73 | 0.82 | 49 | empty |
| 3 | 92 | 0.52 | 0.83 | 26 | empty |
| 4 | 179 | 0.52 | 0.78 | 29 | empty |
| 5 | 81 | 0.50 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 609 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 400 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6WJQ · Crystal structure of WDR5 in complex with the WIN peptide of PDPK1 · 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
- Every structure of UniProt P61964
- Every structure of UniProt O15530
- Elsewhere: RCSB PDB 6WJQ · PDBe 6WJQ · UniProt P61964 · UniProt O15530
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