MolNFT v1 · #142466 · protein + DNA
Structure of histone demethylase REF6 complexed with DNA
6A57 · Lysine-specific demethylase REF6: “Structure of histone demethylase REF6 complexed with DNA”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.57). MolNFT v1 #142466 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6A57
- Type
- protein + DNA
- Length
- 163 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase REF6; DNA (5'-D(*CP*TP*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*GP*TP*…
- EC
- 1.14.11.-
- UniProt
- Q9STM3
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase REF6 (EC 1.14.11.-) | protein | 131 | 31% helix, 9% strand | Q9STM3 |
| B | DNA (5'-D(*CP*TP*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*GP*TP*C)- 3') | dna | 16 | — | — |
| C | DNA (5'-D(*GP*GP*AP*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*AP*A)- 3') | dna | 16 | — | — |
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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.57 | 0.78 | 24 | empty |
| 2 | 64 | 0.30 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 806 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 659 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–C · 365 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6A57 · Structure of histone demethylase REF6 complexed with DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9STM3 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase REF6 (Q9STM3) · a predicted model of the same protein · chain A against A, TM-score 0.73
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 Q9STM3
- Elsewhere: RCSB PDB 6A57 · PDBe 6A57 · UniProt Q9STM3
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