MolNFT v1 · #162208 · protein + DNA
Structure of LSD2/NPAC-LINKER/NUCLEOSOME core particle complex: class 3
6R25 · Lysine-specific histone demethylase 1B: “Structure of LSD2/NPAC-LINKER/NUCLEOSOME core particle complex: class 3”. Electron microscopy, 2 ligands (FAD, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #162208 on GenesisL1: 3D…
- PDB
- 6R25
- Type
- protein + DNA
- Length
- 1,838 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1B; Npac; Histone H3; H4; Histone H2A; H2B; DNA…
- EC
- 1.-.-.-
- UniProt
- Q8NB78, A0A310TTQ1, Q6AZJ8
- Ligands
- FAD, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 13 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Lysine-specific histone demethylase 1B (EC 1.-.-.-) | protein | 737 | 36% helix, 16% strand | Q8NB78 |
| L | Npac | protein | 12 | 25% helix, 0% strand | — |
| M | Histone H3 | protein | 26 | 12% helix, 8% strand | A0A310TTQ1 |
| A | Histone H3 | protein | 99 | 66% helix, 3% strand | A0A310TTQ1 |
| B | H4 | protein | 79 | 58% helix, 8% strand | — |
| C | Histone H2A | protein | 104 | 48% helix, 5% strand | Q6AZJ8 |
| D | H2B | protein | 97 | 68% helix, 3% strand | — |
| E | Histone H3 | protein | 99 | 62% helix, 4% strand | A0A310TTQ1 |
| F | H4 | protein | 80 | 61% helix, 8% strand | — |
| G | Histone H2A | protein | 113 | 47% helix, 6% strand | Q6AZJ8 |
| H | H2B | protein | 98 | 69% helix, 4% strand | — |
| I | DNA (147-mer) | dna | 147 | — | — |
| J | DNA (147-mer) | dna | 147 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.85 | 0.96 | 60 | FAD |
| 2 | 1074 | 0.83 | 0.84 | 108 | empty |
| 3 | 776 | 0.79 | 0.82 | 80 | empty |
| 4 | 296 | 0.74 | 0.87 | 33 | empty |
| 5 | 54 | 0.73 | 0.99 | 20 | empty |
Interfaces
41 interfaces between chains.
- I–J · 6634 Ų buried · 583 hydrogen bonds · nucleic-nucleic
- G–H · 2606 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2479 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2467 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2370 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6R25 · Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3 · the same entry in another collection · chain J against J, 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 Q8NB78
- Every structure of UniProt A0A310TTQ1
- Every structure of UniProt Q6AZJ8
- Elsewhere: RCSB PDB 6R25 · PDBe 6R25 · UniProt Q8NB78 · UniProt A0A310TTQ1 · UniProt Q6AZJ8
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