MolNFT v1 · #93588 · protein
Crystal structure of human SPINDLIN1 in complex with a histone H3K4(ME3) peptide
4H75 · Spindlin-1: “Crystal structure of human SPINDLIN1 in complex with a histone H3K4(ME3) peptide”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.48). MolNFT v1 #93588 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4H75
- Type
- protein
- Length
- 207 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindlin-1; Histone H3
- UniProt
- Q9Y657, Q5TEC6
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spindlin-1 | protein | 199 | 7% helix, 47% strand | Q9Y657 |
| B | Histone H3 | protein | 8 | 0% helix, 25% strand | Q5TEC6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.48 | 0.83 | 11 | NHE |
| 2 | 54 | 0.34 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 683 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 4H75 · Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y657 · AlphaFold monomer V2.0 prediction for spindlin-1 (Q9Y657) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q5TEC6 · AlphaFold monomer V2.0 prediction for histone HIST2H3PS2 (Q5TEC6) · a predicted model of the same protein · chain B against A, TM-score 0.46
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 Q9Y657
- Every structure of UniProt Q5TEC6
- Elsewhere: RCSB PDB 4H75 · PDBe 4H75 · UniProt Q9Y657 · UniProt Q5TEC6
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