MolNFT v1 · #142482 · protein + DNA
Crystal structure of arabidopsis thaliana SUVH6 in complex with methylated DNA
6A5N · Histone-lysine N-methyltransferase, H3 lysine-9 specific…: “Crystal structure of arabidopsis thaliana SUVH6 in complex with methylated DNA”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.80). MolNFT v1 #142482 on…
- PDB
- 6A5N
- Type
- protein + DNA
- Length
- 528 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6; DNA…
- EC
- 2.1.1.43
- UniProt
- Q8VZ17
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6 (EC 2.1.1.43) | protein | 502 | 17% helix, 25% strand | Q8VZ17 |
| C | DNA (5'-D(*GP*AP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*T)- 3') | dna | 13 | — | — |
| D | DNA (5'-D(*CP*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*T)-3') | dna | 13 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.80 | 0.82 | 81 | empty |
| 2 | 963 | 0.73 | 0.77 | 78 | empty |
| 3 | 254 | 0.67 | 0.84 | 31 | empty |
| 4 | 309 | 0.62 | 0.79 | 50 | empty |
| 5 | 74 | 0.41 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 832 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–D · 573 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–D · 484 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6A5N · Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VZ17 · 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 0.95
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 Q8VZ17
- Elsewhere: RCSB PDB 6A5N · PDBe 6A5N · UniProt Q8VZ17
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