MolNFT v1 · #163297 · protein + DNA
Nucleosome-CHD4 complex structure (two CHD4 copies)
6RYU · Histone H3.2: “Nucleosome-CHD4 complex structure (two CHD4 copies)”. Electron microscopy, 3 ligands (ANP, ZN, MG), 20 pockets (best druggability 0.87). MolNFT v1 #163297 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RYU
- Type
- protein + DNA
- Length
- 2,478 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B 1.1; DNA (149-mer)…
- EC
- 3.6.4.12
- UniProt
- P84233, P62799, P06897, P02281, Q14839
- Ligands
- ANP, ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 10 distinct chains · 44% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 97 | 59% helix, 3% strand | P84233 |
| B, F | Histone H4 | protein | 87 | 45% helix, 6% strand | P62799 |
| C | Histone H2A type 1 | protein | 103 | 53% helix, 5% strand | P06897 |
| D | Histone H2B 1.1 | protein | 95 | 74% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 97 | 54% helix, 3% strand | P84233 |
| G | Histone H2A type 1 | protein | 105 | 48% helix, 4% strand | P06897 |
| H | Histone H2B 1.1 | protein | 93 | 74% helix, 2% strand | P02281 |
| I | DNA (149-mer) | dna | 149 | — | — |
| J | DNA (149-mer) | dna | 149 | — | — |
| W, V | Chromodomain-helicase-DNA-binding protein 4,CHD4, chromodomain-helicase-DNA-binding protein 4 (EC 3.6.4.12) | protein | 708 | 31% helix, 14% strand | Q14839 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains W, V
- ZN · Zinc ion · metal · 4 copies · chains W, V
- MG · Magnesium ion · metal · 2 copies · chains W, V
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 | 687 | 0.87 | 0.91 | 73 | empty |
| 2 | 650 | 0.84 | 0.89 | 76 | empty |
| 3 | 790 | 0.81 | 0.84 | 81 | empty |
| 4 | 718 | 0.79 | 0.84 | 66 | empty |
| 5 | 465 | 0.77 | 0.86 | 45 | empty |
Interfaces
44 interfaces between chains.
- I–J · 6999 Ų buried · 898 hydrogen bonds · nucleic-nucleic
- G–H · 2634 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2622 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2566 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2556 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6RYU · Nucleosome-CHD4 complex structure (two CHD4 copies) · the same entry in another collection · chain V against V, 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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Every structure of UniProt Q14839
- Elsewhere: RCSB PDB 6RYU · PDBe 6RYU · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt Q14839
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