MolNFT v1 · #108153 · protein
1.86 a structure of human spindlin-4 protein in complex with histone H3K4ME3 peptide
4UY4: “1.86 a structure of human spindlin-4 protein in complex with histone H3K4ME3 peptide”. X-ray diffraction, 1 pocket (best druggability 0.33). MolNFT v1 #108153 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UY4
- Type
- protein
- Length
- 423 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindlin-4; Histone H3K4ME3
- UniProt
- Q56A73
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spindlin-4 | protein | 203 | 6% helix, 45% strand | Q56A73 |
| B | Spindlin-4 | protein | 208 | 6% helix, 47% strand | Q56A73 |
| C, D | Histone H3K4ME3 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.33 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–D · 499 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 468 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4UY4 · 1.86 A structure of human Spindlin-4 protein in complex with histone H3K4me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q56A73 · AlphaFold monomer V2.0 prediction for spindlin-4 (Q56A73) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q56A73
- Elsewhere: RCSB PDB 4UY4 · PDBe 4UY4 · UniProt Q56A73
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