Research workbench
Crystal structure of kryptonite in complex with mchh DNA and sah
Analyse Crystal structure of kryptonite in complex with mchh DNA and sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QEN
- Type
- protein + DNA
- Length
- 496 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4; DNA…
- EC
- 2.1.1.43
- UniProt
- Q8GZB6
- Ligands
- SAH, ZN
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 (EC 2.1.1.43) | protein | 472 | 16% helix, 27% strand | Q8GZB6 |
| C | DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM) P*AP*TP*CP*AP*GP*TP*AP*T)-3') | dna | 11 | — | — |
| D | DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)- 3') | dna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.71 | 0.82 | 53 | empty |
| 2 | 335 | 0.65 | 0.80 | 36 | empty |
| 3 | 222 | 0.60 | 0.81 | 40 | empty |
| 4 | 290 | 0.60 | 0.78 | 41 | SAH |
| 5 | 121 | 0.52 | 0.82 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 817 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 649 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–D · 493 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4QEN · crystal structure of KRYPTONITE in complex with mCHH DNA and SAH · the same entry in another collection · chain A against A, TM-score 1.00
- Q8GZB6 · 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 1.00
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 Q8GZB6
- Elsewhere: RCSB PDB 4QEN · PDBe 4QEN · UniProt Q8GZB6
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