Research workbench
Composite model of a CHD1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A cryo-EM maps
Analyse Composite model of a CHD1-nucleosome complex in the nucleotide-free state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TN2
- Type
- protein + DNA
- Length
- 1,974 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A type 1; Histone H2B; DNA tracking strand; DNA lagging…
- EC
- 3.6.4.-
- UniProt
- A0A310TTQ1, P62799, P06897, A0A1L8FQ56, P32657
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 96 | 61% helix, 5% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 89 | 54% helix, 8% strand | P62799 |
| C | Histone H2A type 1 | protein | 106 | 54% helix, 7% strand | P06897 |
| D | Histone H2B | protein | 96 | 71% helix, 4% strand | A0A1L8FQ56 |
| E | Histone H3 | protein | 97 | 63% helix, 4% strand | A0A310TTQ1 |
| F | Histone H4 | protein | 85 | 56% helix, 8% strand | P62799 |
| G | Histone H2A type 1 | protein | 98 | 56% helix, 7% strand | P06897 |
| H | Histone H2B | protein | 92 | 75% helix, 4% strand | A0A1L8FQ56 |
| I | DNA tracking strand | dna | 160 | — | — |
| J | DNA lagging strand | dna | 160 | — | — |
| W | Chromo domain-containing protein 1 (EC 3.6.4.-) | protein | 895 | 43% helix, 12% strand | P32657 |
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 | 951 | 0.86 | 0.88 | 79 | empty |
| 2 | 1045 | 0.78 | 0.80 | 82 | empty |
| 3 | 587 | 0.74 | 0.81 | 53 | empty |
| 4 | 328 | 0.71 | 0.84 | 38 | empty |
| 5 | 1175 | 0.71 | 0.75 | 81 | empty |
Interfaces
40 interfaces between chains.
- I–J · 7246 Ų buried · 541 hydrogen bonds · nucleic-nucleic
- E–F · 2618 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2598 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 2588 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2471 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7TN2 · Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from… · the same entry in another collection · chain W against W, TM-score 1.00
- P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain G against A, TM-score 0.96
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 A0A1L8FQ56
- Every structure of UniProt P32657
- Elsewhere: RCSB PDB 7TN2 · PDBe 7TN2 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt P06897 · UniProt A0A1L8FQ56 · UniProt P32657
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