Research workbench
Crystal structure of yeast SWR1-Z domain in complex with H2A.Z-H2B dimer
Analyse Crystal structure of yeast SWR1-Z domain in complex with H2A.Z-H2B dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M6B
- Type
- protein
- Length
- 418 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera protein of histone H2B.1 and histone H2A.Z; Helicase SWR1
- EC
- 3.6.4.12
- UniProt
- P02293, Q12692, Q05471
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera protein of histone H2B.1 and histone H2A.Z | protein | 185 | 73% helix, 5% strand | P02293, Q12692 |
| C, F | Helicase SWR1 (EC 3.6.4.12) | protein | 23 | 17% helix, 4% strand | Q05471 |
| D | Chimera protein of histone H2B.1 and histone H2A.Z | protein | 187 | 72% helix, 5% strand | P02293, Q12692 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.71 | 0.91 | 20 | empty |
| 2 | 61 | 0.30 | 0.75 | 16 | empty |
Interfaces
6 interfaces between chains.
- D–F · 1027 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1010 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 255 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 255 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 118 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4M6B · Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer · the same entry in another collection · chain A against A, TM-score 1.00
- P02293 · AlphaFold monomer V2.0 prediction for histone H2B.1 (P02293) · a predicted model of the same protein · chain A against A, TM-score 0.49
- Q12692 · AlphaFold monomer V2.0 prediction for histone H2A.Z (Q12692) · a predicted model of the same protein · chain A against A, TM-score 0.46
- Q05471 · AlphaFold monomer V2.0 prediction for helicase SWR1 (Q05471) · a predicted model of the same protein · chain C against A, TM-score 0.21
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 P02293
- Every structure of UniProt Q12692
- Every structure of UniProt Q05471
- Elsewhere: RCSB PDB 4M6B · PDBe 4M6B · UniProt P02293 · UniProt Q12692 · UniProt Q05471
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