Research workbench
REF6 ZNF2-4-NAC004-MC1 complex
Analyse REF6 ZNF2-4-NAC004-MC1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JNN
- Type
- protein + DNA
- Length
- 451 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase REF6; DNA (5'-D(*TP*TP*(5CM)P*TP*CP*TP*GP*TP*TP*TP*TP*G)-3')…
- EC
- 1.14.11.-
- UniProt
- Q9STM3
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, N | Lysine-specific demethylase REF6 (EC 1.14.11.-) | protein | 89 | 37% helix, 13% strand | Q9STM3 |
| D, F, I, L | DNA (5'-D(*TP*TP*(5CM)P*TP*CP*TP*GP*TP*TP*TP*TP*G)-3') | dna | 12 | — | — |
| C, E, H, K | DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3') | dna | 12 | — | — |
| G | Lysine-specific demethylase REF6 (EC 1.14.11.-) | protein | 88 | 39% helix, 8% strand | Q9STM3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, N, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.75 | 0.80 | 59 | empty |
| 2 | 894 | 0.75 | 0.79 | 78 | empty |
| 3 | 450 | 0.62 | 0.76 | 46 | empty |
| 4 | 221 | 0.57 | 0.79 | 24 | empty |
| 5 | 190 | 0.56 | 0.80 | 22 | empty |
Interfaces
27 interfaces between chains.
- L–G · 770 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–F · 755 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 753 Ų buried · 7 hydrogen bonds · protein-nucleic
- I–N · 732 Ų buried · 4 hydrogen bonds · protein-nucleic
- F–E · 538 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6JNN · REF6 ZnF2-4-NAC004-mC1 complex · the same entry in another collection · chain G against G, 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 Q9STM3
- Elsewhere: RCSB PDB 6JNN · PDBe 6JNN · UniProt Q9STM3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.