Research workbench
The crosslinked complex of iswi-nucleosome in the ADP-bound state
Analyse The crosslinked complex of iswi-nucleosome in the ADP-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IRO
- Type
- protein + DNA
- Length
- 1,554 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iswi chromatin-remodeling complex ATPase ISW1; Histone H3; Histone H4; Histone H2A…
- EC
- 3.6.4.-
- UniProt
- P38144, A0A310TTQ1, P62799, Q6AZJ8, P02281
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 9 distinct chains · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Iswi chromatin-remodeling complex ATPase ISW1 (EC 3.6.4.-) | protein | 496 | 42% helix, 9% strand | P38144 |
| A | Histone H3 | protein | 98 | 62% helix, 4% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 87 | 60% helix, 7% strand | P62799 |
| C, G | Histone H2A | protein | 107 | 50% helix, 5% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 93 | 74% helix, 3% strand | P02281 |
| E | Histone H3 | protein | 95 | 62% helix, 4% strand | A0A310TTQ1 |
| F | Histone H4 | protein | 86 | 59% helix, 7% strand | P62799 |
| I | DNA (167-mer) | dna | 146 | — | — |
| J | DNA (167-mer) | dna | 146 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains L
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 | 1135 | 0.84 | 0.85 | 85 | ADP |
| 2 | 1152 | 0.79 | 0.81 | 94 | empty |
| 3 | 137 | 0.77 | 0.95 | 22 | empty |
| 4 | 106 | 0.74 | 0.94 | 19 | empty |
| 5 | 291 | 0.72 | 0.86 | 31 | empty |
Interfaces
39 interfaces between chains.
- I–J · 6584 Ų buried · 453 hydrogen bonds · nucleic-nucleic
- C–D · 2602 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 2584 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 2533 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 2464 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6IRO · the crosslinked complex of ISWI-nucleosome in the ADP-bound state · the same entry in another collection · chain J against J, 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 L against A, TM-score 0.81
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 P38144
- Every structure of UniProt A0A310TTQ1
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 6IRO · PDBe 6IRO · UniProt P38144 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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