Research workbench
Crystal structure of human SPINDLIN1 bound to histone H3(K4ME3-R8ME2S) peptide
Analyse Crystal structure of human SPINDLIN1 bound to histone H3(K4ME3-R8ME2S) peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MZH
- Type
- protein
- Length
- 207 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindlin-1; Peptide from histone H3.2
- UniProt
- Q9Y657, Q71DI3
- Ligands
- MG
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spindlin-1 | protein | 200 | 7% helix, 49% strand | Q9Y657 |
| B | Peptide from histone H3.2 | protein | 7 | 0% helix, 29% strand | Q71DI3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 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 | 64 | 0.32 | 0.76 | 15 | empty |
| 2 | 60 | 0.28 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 574 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 4MZH · Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide · the same entry in another collection · chain B against B, 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 0.94
- Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain B against A, TM-score 0.57
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 Q71DI3
- Elsewhere: RCSB PDB 4MZH · PDBe 4MZH · UniProt Q9Y657 · UniProt Q71DI3
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