MolNFT v1 · #173377 · protein
Structural characterisation of WDR5:CS-VIP8 interaction in cis state 2
7AXP · Wd repeat-containing protein 5: “Structural characterisation of WDR5:CS-VIP8 interaction in cis state 2”. X-ray diffraction, 3 ligands (ALQ, EDN, S7Z), 1 pocket (best druggability 0.70). MolNFT v1 #173377 on GenesisL1: 3D structure…
- PDB
- 7AXP
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; Cs-VIP8
- UniProt
- P61964
- Ligands
- ALQ, EDN, S7Z
- Pockets
- 1 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 53% strand | P61964 |
| B | Cs-VIP8 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ALQ · 2-methyl-propionic acid · ligand · chains A, B
- EDN · Ethane-1,2-diamine · ligand · chains B
- S7Z · (E)-(4-((2,6-difluoro-4-(hydroxymethyl)phenyl) diazenyl)-2,6-difluorophenyl)methanol · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.70 | 0.81 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 402 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 d-amino (nonstandard, D-amino acid).
Compared structures
- 7AXP · Structural characterisation of WDR5:CS-VIP8 interaction in cis state 2 · 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
- Elsewhere: RCSB PDB 7AXP · PDBe 7AXP · UniProt P61964
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