MolNFT v1 · #95598 · protein
Crystal structure of SHH1 sawadee domain in complex with H3K9ME1 peptide
4IUU · Sawadee homeodomain homolog 1: “Crystal structure of SHH1 sawadee domain in complex with H3K9ME1 peptide”. X-ray diffraction, 2 ligands (CVM, ZN), 2 pockets (best druggability 0.41). MolNFT v1 #95598 on GenesisL1: 3D structure…
- PDB
- 4IUU
- Type
- protein
- Length
- 269 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 0.41
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sawadee homeodomain homolog 1 | protein | 127 | 10% helix, 50% strand | Q9XI47 |
| B | Sawadee homeodomain homolog 1 | protein | 134 | 10% helix, 48% strand | Q9XI47 |
| C | Histone H3.2, H3(1-15)K9ME3 | protein | 8 | 0% helix, 13% 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 | 112 | 0.41 | 0.76 | 24 | empty |
| 2 | 57 | 0.36 | 0.79 | 10 | empty |
Interfaces
2 interfaces between chains.
- B–C · 653 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 181 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 4IUU · Crystal structure of SHH1 SAWADEE domain in complex with H3K9me1 peptide · the same entry in another collection · chain A against A, 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 A 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 0.53
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 4IUU · PDBe 4IUU · UniProt Q9XI47 · UniProt P59226
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