Research workbench
Crystal structure of SHH1 sawadee domain in complex with H3K4ME1K9ME1 peptide
Analyse Crystal structure of SHH1 sawadee domain in complex with H3K4ME1K9ME1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IUV
- Type
- protein
- Length
- 272 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sawadee homeodomain homolog 1; Histone H3.2, H3(1-15)K9ME3
- UniProt
- Q9XI47, P59226
- Ligands
- CVM, ZN
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Sawadee homeodomain homolog 1 | protein | 129 | 10% helix, 51% strand | Q9XI47 |
| A | Sawadee homeodomain homolog 1 | protein | 134 | 9% helix, 48% strand | Q9XI47 |
| C | Histone H3.2, H3(1-15)K9ME3 | protein | 9 | 0% helix, 11% strand | P59226 |
Ligands and binding sites
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 | 144 | 0.48 | 0.78 | 30 | empty |
| 2 | 82 | 0.33 | 0.74 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–C · 723 Ų buried · 13 hydrogen bonds · protein-protein
- B–A · 274 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 4IUV · crystal structure of SHH1 SAWADEE domain in complex with H3K4me1K9me1 peptide · the same entry in another collection · chain B against B, TM-score 1.00
- Q9XI47 · AlphaFold monomer V2.0 prediction for protein sawadee homeodomain homolog 1 (Q9XI47) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P59226 · AlphaFold monomer V2.0 prediction for histone H3.2 (P59226) · a predicted model of the same protein · chain C against A, TM-score 0.45
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 Q9XI47
- Every structure of UniProt P59226
- Elsewhere: RCSB PDB 4IUV · PDBe 4IUV · UniProt Q9XI47 · UniProt P59226
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