Research workbench
X-ray structure of WDR5DELTA24 bound to the KAPOSI'S sarcoma herpesvirus lana win motif peptide
Analyse X-ray structure of WDR5DELTA24 bound to the KAPOSI'S sarcoma herpesvirus lana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BCY
- Type
- protein
- Length
- 618 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; Orf 73
- UniProt
- P61964, Q76SB0
- Ligands
- ACE
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 301 | 0% helix, 51% strand | P61964 |
| B | Wd repeat-containing protein 5 | protein | 303 | 0% helix, 51% strand | P61964 |
| P, Q | Orf 73 | protein | 7 | 0% helix, 0% strand | Q76SB0 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, P, A, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.73 | 0.82 | 45 | empty |
| 2 | 488 | 0.72 | 0.82 | 45 | empty |
| 3 | 475 | 0.65 | 0.78 | 54 | empty |
| 4 | 50 | 0.37 | 0.80 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–P · 616 Ų buried · 7 hydrogen bonds · protein-protein
- A–Q · 559 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 186 Ų buried · 3 hydrogen bonds · protein-protein
- A–P · 112 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7BCY · X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif… · 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 Q76SB0
- Elsewhere: RCSB PDB 7BCY · PDBe 7BCY · UniProt P61964 · UniProt Q76SB0
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