Research workbench
Crystal structure of SUVH5 sra-fully methylated cg DNA complex in space group P6122
Analyse Crystal structure of SUVH5 sra-fully methylated cg DNA complex in space group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q0C
- Type
- protein + DNA
- Length
- 312 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5; DNA…
- EC
- 2.1.1.43
- UniProt
- O82175
- Ligands
- MG
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5 (EC 2.1.1.43) | protein | 147 | 13% helix, 35% strand | O82175 |
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5 (EC 2.1.1.43) | protein | 144 | 13% helix, 36% strand | O82175 |
| C | DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*TP*T)-3') | dna | 10 | — | — |
| B | DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*TP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.74 | 0.98 | 12 | empty |
| 2 | 147 | 0.60 | 0.84 | 27 | empty |
| 3 | 108 | 0.56 | 0.85 | 25 | empty |
| 4 | 76 | 0.29 | 0.73 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 590 Ų buried · 18 hydrogen bonds · protein-nucleic
- X–C · 576 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–B · 463 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- X–B · 377 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–C · 262 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3Q0C · Crystal structure of SUVH5 SRA-fully methylated CG DNA complex in space group P6122 · the same entry in another collection · chain X against X, 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 0.96
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 3Q0C · PDBe 3Q0C · UniProt O82175
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