Research workbench
Crystal structure of SUVH5 sra bound to fully hydroxymethylated cg DNA
Analyse Crystal structure of SUVH5 sra bound to fully hydroxymethylated cg DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YGI
- Type
- protein + DNA
- Length
- 160 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5; Polydeoxyribonucleotide
- EC
- 2.1.1.43
- UniProt
- O82175
- Ligands
- MG
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5 (EC 2.1.1.43) | protein | 150 | 12% helix, 34% strand | O82175 |
| B | Polydeoxyribonucleotide | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.46 | 0.83 | 18 | empty |
| 2 | 71 | 0.33 | 0.76 | 14 | empty |
| 3 | 64 | 0.27 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 592 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4YGI · Crystal Structure of SUVH5 SRA bound to fully hydroxymethylated CG DNA · the same entry in another collection · chain A against A, TM-score 1.00
- O82175 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase, H3 lysine-9… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O82175
- Elsewhere: RCSB PDB 4YGI · PDBe 4YGI · UniProt O82175
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