Research workbench
The crosslinked complex of iswi-nucleosome in the ADP.BEF-bound state
Analyse The crosslinked complex of iswi-nucleosome in the ADP.BEF-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JYL
- Type
- protein + DNA
- Length
- 1,557 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B 1.1; DNA (167-mer); Iswi…
- EC
- 3.6.4.-
- UniProt
- A0A310TTQ1, P62799, Q6AZJ8, P02281, P38144
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 54% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 98 | 64% helix, 2% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 88 | 58% helix, 5% strand | P62799 |
| C, G | Histone H2A | protein | 107 | 54% helix, 5% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 93 | 74% helix, 2% strand | P02281 |
| E | Histone H3 | protein | 95 | 65% helix, 3% strand | A0A310TTQ1 |
| F | Histone H4 | protein | 80 | 64% helix, 8% strand | P62799 |
| I | DNA (167-mer) | dna | 146 | — | — |
| J | DNA (167-mer) | dna | 146 | — | — |
| K | Iswi chromatin-remodeling complex ATPase ISW1 (EC 3.6.4.-) | protein | 504 | 44% helix, 9% strand | P38144 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains K
- BEF · Beryllium trifluoride ion · ligand · chains K
- MG · Magnesium ion · metal · chains 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 | 516 | 0.85 | 0.91 | 62 | empty |
| 2 | 833 | 0.76 | 0.80 | 69 | empty |
| 3 | 270 | 0.75 | 0.88 | 60 | empty |
| 4 | 579 | 0.75 | 0.82 | 60 | empty |
| 5 | 354 | 0.75 | 0.86 | 47 | empty |
Interfaces
39 interfaces between chains.
- I–J · 6597 Ų buried · 443 hydrogen bonds · nucleic-nucleic
- G–H · 2605 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2587 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2500 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2495 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6JYL · The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state · the same entry in another collection · chain K against K, TM-score 1.00
- P38144 · AlphaFold monomer V2.0 prediction for iswi chromatin-remodeling complex ATPase ISW1… · a predicted model of the same protein · chain K against A, TM-score 0.91
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 Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt P38144
- Elsewhere: RCSB PDB 6JYL · PDBe 6JYL · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P38144
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