Research workbench
Conserved N-terminal domain of the yeast histone chaperone ASF1 in complex with the C-terminal fragment of RAD53
Analyse Conserved N-terminal domain of the yeast histone chaperone ASF1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YGV
- Type
- protein
- Length
- 672 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone chaperone ASF1; SERINE/THREONINE-protein kinase RAD53
- EC
- 2.7.11.1
- UniProt
- P32447, P22216
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone chaperone ASF1 | protein | 154 | 7% helix, 50% strand | P32447 |
| B, C | Histone chaperone ASF1 | protein | 155 | 2% helix, 50% strand | P32447 |
| D | Histone chaperone ASF1 | protein | 152 | 7% helix, 51% strand | P32447 |
| E | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.11.1) | protein | 19 | 16% helix, 32% strand | P22216 |
| F | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.11.1) | protein | 13 | 0% helix, 31% strand | P22216 |
| G | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.11.1) | protein | 14 | 0% helix, 21% strand | P22216 |
| H | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.11.1) | protein | 10 | 0% helix, 20% strand | P22216 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.73 | 0.90 | 45 | empty |
| 2 | 612 | 0.70 | 0.78 | 79 | empty |
| 3 | 322 | 0.62 | 0.79 | 42 | empty |
| 4 | 56 | 0.55 | 0.89 | 20 | empty |
| 5 | 269 | 0.53 | 0.76 | 41 | empty |
Interfaces
11 interfaces between chains.
- B–D · 1051 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 875 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 842 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 602 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 467 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2YGV · Conserved N-terminal domain of the yeast Histone Chaperone Asf1 in complex with the… · the same entry in another collection · chain H against H, TM-score 1.00
- P32447 · AlphaFold monomer V2.0 prediction for histone chaperone ASF1 (P32447) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 P32447
- Every structure of UniProt P22216
- Elsewhere: RCSB PDB 2YGV · PDBe 2YGV · UniProt P32447 · UniProt P22216
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