MolNFT v1 · #153729 · protein + DNA
REF6 ZNF2-4-NAC004-MC3 complex
6JNM · Lysine-specific demethylase REF6: “REF6 ZNF2-4-NAC004-MC3 complex”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.56). MolNFT v1 #153729 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JNM
- Type
- protein + DNA
- Length
- 226 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase REF6; DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3')…
- EC
- 1.14.11.-
- UniProt
- Q9STM3
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase REF6 (EC 1.14.11.-) | protein | 89 | 38% helix, 11% strand | Q9STM3 |
| D, F | DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3') | dna | 12 | — | — |
| C, E | DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3') | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.56 | 0.80 | 21 | empty |
| 2 | 217 | 0.56 | 0.78 | 22 | empty |
Interfaces
10 interfaces between chains.
- A–D · 736 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–F · 721 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–E · 533 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- D–C · 531 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–C · 459 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 disulfide, 2 modified (disulfide, nucleotide modification).
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 6JNM · PDBe 6JNM · UniProt Q9STM3
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