Research workbench
Nucleosome-CHD4 complex structure (single CHD4 copy)
Analyse Nucleosome-CHD4 complex structure (single CHD4 copy) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RYR
- Type
- protein + DNA
- Length
- 1,761 residues
- Chains
- 11
- 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 0.82
Structure
electron microscopy · 11 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 97 | 65% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 87 | 51% helix, 8% strand | P62799 |
| C | Histone H2A type 1 | protein | 103 | 55% helix, 7% strand | P06897 |
| D | Histone H2B 1.1 | protein | 95 | 71% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 97 | 63% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 78 | 62% helix, 9% strand | P62799 |
| G | Histone H2A type 1 | protein | 105 | 53% helix, 7% strand | P06897 |
| H | Histone H2B 1.1 | protein | 93 | 75% helix, 4% strand | P02281 |
| I | DNA (149-mer) | dna | 149 | — | — |
| J | DNA (149-mer) | dna | 149 | — | — |
| W | Chromodomain-helicase-DNA-binding protein 4,CHROMODOMAIN- helicase-DNA-binding protein 4,CHROMODOMAIN-helicase-DNA-binding protein 4 (EC 3.6.4.12) | protein | 708 | 36% helix, 14% strand | Q14839 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains W
- ZN · Zinc ion · metal · 2 copies · chains W
- MG · Magnesium ion · metal · chains W
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 | 627 | 0.82 | 0.87 | 72 | empty |
| 2 | 810 | 0.80 | 0.84 | 86 | empty |
| 3 | 158 | 0.80 | 0.96 | 20 | empty |
| 4 | 949 | 0.78 | 0.81 | 60 | empty |
| 5 | 452 | 0.74 | 0.84 | 46 | empty |
Interfaces
38 interfaces between chains.
- I–J · 6854 Ų buried · 626 hydrogen bonds · nucleic-nucleic
- G–H · 2615 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2610 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2523 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2491 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6RYR · Nucleosome-CHD4 complex structure (single CHD4 copy) · the same entry in another collection · chain W against W, TM-score 1.00
- Q14839 · AlphaFold monomer V2.0 prediction for chromodomain-helicase-DNA- binding protein 4… · a predicted model of the same protein · chain W against A, TM-score 0.99
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 6RYR · PDBe 6RYR · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281 · UniProt Q14839
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