Research workbench
Structure of LSD2/NPAC-LINKER/NUCLEOSOME core particle complex: class 1, free nuclesome
Analyse Structure of LSD2/NPAC-LINKER/NUCLEOSOME core particle complex: class 1, free… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R1T
- Type
- protein + DNA
- Length
- 1,073 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H2A; Histone H2B; DNA (147-mer)
- UniProt
- A0A310TTQ1, Q6AZJ8, A0A1L8FQ56
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 10 distinct chains · 59% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 99 | 66% helix, 3% strand | A0A310TTQ1 |
| B | Histone H2A | protein | 86 | 53% helix, 7% strand | — |
| C | Histone H2A | protein | 108 | 46% helix, 5% strand | Q6AZJ8 |
| D | Histone H2B | protein | 96 | 69% helix, 3% strand | A0A1L8FQ56 |
| E | Histone H3 | protein | 98 | 62% helix, 4% strand | A0A310TTQ1 |
| F | Histone H2A | protein | 86 | 57% helix, 7% strand | — |
| G | Histone H2A | protein | 111 | 48% helix, 6% strand | Q6AZJ8 |
| H | Histone H2B | protein | 95 | 72% helix, 4% strand | A0A1L8FQ56 |
| I | DNA (147-mer) | dna | 147 | — | — |
| J | DNA (147-mer) | dna | 147 | — | — |
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 | 594 | 0.77 | 0.83 | 58 | empty |
| 2 | 456 | 0.75 | 0.84 | 45 | empty |
| 3 | 405 | 0.74 | 0.85 | 45 | empty |
| 4 | 821 | 0.72 | 0.78 | 52 | empty |
| 5 | 407 | 0.71 | 0.83 | 36 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6641 Ų buried · 584 hydrogen bonds · nucleic-nucleic
- G–H · 2602 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2504 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2477 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2440 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6R1T · Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 1, free nuclesome · the same entry in another collection · chain A against A, 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 A0A310TTQ1
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt A0A1L8FQ56
- Elsewhere: RCSB PDB 6R1T · PDBe 6R1T · UniProt A0A310TTQ1 · UniProt Q6AZJ8 · UniProt A0A1L8FQ56
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