MolNFT v1 · #168544 · protein
Crystal structure of WDR5 in complex with the win peptide of PDPK1
6WJQ · Wd repeat-containing protein 5: “Crystal structure of WDR5 in complex with the win peptide of PDPK1”. X-ray diffraction, 1 ligand (ACE), 6 pockets (best druggability 0.83). MolNFT v1 #168544 on GenesisL1: 3D structure, binding sites…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.