MolNFT v1 · #153728 · protein + DNA
REF6 ZNF2-4-NAC004 complex
6JNL · Lysine-specific demethylase REF6: “REF6 ZNF2-4-NAC004 complex”. X-ray diffraction, 3 ligands (DA, ZN, MG), 1 pocket (best druggability 0.57). MolNFT v1 #153728 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JNL
- Type
- protein + DNA
- Length
- 112 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase REF6; DNA (5'-D(*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*G)-3'); DNA…
- EC
- 1.14.11.-
- UniProt
- Q9STM3
- Ligands
- DA, ZN, MG
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase REF6 (EC 1.14.11.-) | protein | 89 | 38% helix, 13% strand | Q9STM3 |
| D | DNA (5'-D(*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*G)-3') | dna | 12 | — | — |
| C | DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*A)-3') | dna | 11 | — | — |
Ligands and binding sites
- DA · 2'-deoxyadenosine-5'-monophosphate · ligand · chains D, C
- ZN · Zinc ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.57 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–D · 718 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–C · 498 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- A–C · 443 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 6JNL · PDBe 6JNL · UniProt Q9STM3
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