Research workbench
Cryo-EM structure of the ATPase domain of chromatin remodeling factor iswi bound to the nucleosome
Analyse Cryo-EM structure of the ATPase domain of chromatin remodeling factor iswi… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PWF
- Type
- protein + DNA
- Length
- 1,500 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B; DNA (147-mer); Chromatin remodeling…
- UniProt
- P02299, A0A0B4KFZ9, P84051, P02283, G0S9L5
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 43% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3 | protein | 96 | 58% helix, 4% strand | P02299 |
| B | Histone H4 | protein | 88 | 49% helix, 6% strand | A0A0B4KFZ9 |
| C | Histone H2A | protein | 104 | 40% helix, 5% strand | P84051 |
| D | Histone H2B | protein | 92 | 57% helix, 4% strand | P02283 |
| F | Histone H4 | protein | 79 | 49% helix, 6% strand | A0A0B4KFZ9 |
| G | Histone H2A | protein | 105 | 37% helix, 2% strand | P84051 |
| H | Histone H2B | protein | 94 | 56% helix, 1% strand | P02283 |
| I | DNA (147-mer) | dna | 146 | — | — |
| J | DNA (147-mer) | dna | 146 | — | — |
| K | Chromatin remodeling factor iswi | protein | 454 | 34% helix, 10% strand | G0S9L5 |
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 | 1100 | 0.84 | 0.85 | 94 | empty |
| 2 | 605 | 0.79 | 0.84 | 74 | empty |
| 3 | 431 | 0.72 | 0.83 | 48 | empty |
| 4 | 286 | 0.70 | 0.85 | 34 | empty |
| 5 | 381 | 0.69 | 0.82 | 60 | empty |
Interfaces
40 interfaces between chains.
- I–J · 6674 Ų buried · 540 hydrogen bonds · nucleic-nucleic
- G–H · 2709 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2645 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2515 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2508 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6PWF · Cryo-EM structure of the ATPase domain of chromatin remodeling factor ISWI bound to the… · the same entry in another collection · chain K against K, TM-score 1.00
- P02299 · AlphaFold monomer V2.0 prediction for histone H3 (P02299) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P02299
- Every structure of UniProt A0A0B4KFZ9
- Every structure of UniProt P84051
- Every structure of UniProt P02283
- Every structure of UniProt G0S9L5
- Elsewhere: RCSB PDB 6PWF · PDBe 6PWF · UniProt P02299 · UniProt A0A0B4KFZ9 · UniProt P84051 · UniProt P02283 · UniProt G0S9L5
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