MolNFT v1 · #167894 · protein + DNA
Crystal structure of the LSD1/COREST histone demethylase bound to its nucleosome substrate
6VYP · Histone H3: “Crystal structure of the LSD1/COREST histone demethylase bound to its nucleosome substrate”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.86). MolNFT v1 #167894 on GenesisL1: 3D structure, binding…
- PDB
- 6VYP
- Type
- protein + DNA
- Length
- 5,478 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A type 1; Histone H2B 1.1; DNA (191-mer)…
- EC
- 1.-.-.-
- UniProt
- A0A310TTQ1, P62799, P06897, P02281, O60341, Q9UKL0
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 17 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 110 | 58% helix, 4% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 81 | 57% helix, 9% strand | P62799 |
| C, c | Histone H2A type 1 | protein | 103 | 54% helix, 7% strand | P06897 |
| D | Histone H2B 1.1 | protein | 92 | 75% helix, 4% strand | P02281 |
| E | Histone H3 | protein | 110 | 61% helix, 4% strand | A0A310TTQ1 |
| F, f | Histone H4 | protein | 78 | 64% helix, 9% strand | P62799 |
| G | Histone H2A type 1 | protein | 105 | 53% helix, 7% strand | P06897 |
| H, h | Histone H2B 1.1 | protein | 93 | 74% helix, 4% strand | P02281 |
| I, i | DNA (191-mer) | dna | 191 | — | — |
| J, j | DNA (191-mer) | dna | 191 | — | — |
| a | Histone H3 | protein | 94 | 67% helix, 4% strand | A0A310TTQ1 |
| b | Histone H4 | protein | 80 | 60% helix, 9% strand | P62799 |
| d | Histone H2B 1.1 | protein | 91 | 76% helix, 4% strand | P02281 |
| e | Histone H3 | protein | 103 | 62% helix, 4% strand | A0A310TTQ1 |
| g | Histone H2A type 1 | protein | 104 | 54% helix, 7% strand | P06897 |
| M, m, K, k | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 666 | 44% helix, 16% strand | O60341 |
| N, n, L, l | Rest corepressor 1 | protein | 133 | 65% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains E, M, e, m, A, K, k
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 | 403 | 0.86 | 0.94 | 62 | FAD |
| 2 | 368 | 0.85 | 0.94 | 59 | FAD |
| 3 | 406 | 0.85 | 0.92 | 61 | FAD |
| 4 | 1085 | 0.84 | 0.85 | 113 | FAD |
| 5 | 950 | 0.84 | 0.85 | 117 | empty |
Interfaces
108 interfaces between chains.
- I–J · 8644 Ų buried · 725 hydrogen bonds · nucleic-nucleic
- i–j · 8636 Ų buried · 728 hydrogen bonds · nucleic-nucleic
- G–H · 2679 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2677 Ų buried · 17 hydrogen bonds · protein-protein
- g–h · 2667 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 cofactor (flavinylation).
Compared structures
- 6VYP · Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate · 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 A0A310TTQ1
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Every structure of UniProt O60341
- Every structure of UniProt Q9UKL0
- Elsewhere: RCSB PDB 6VYP · PDBe 6VYP · UniProt A0A310TTQ1 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt O60341 · UniProt Q9UKL0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.