Research workbench
Crystal structure of NURF55 in complex with SU(Z)12
Analyse Crystal structure of NURF55 in complex with SU(Z)12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YB8
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein SU(Z)12; Probable histone-binding protein CAF1
- UniProt
- Q9NJG9, Q24572
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein SU(Z)12 | protein | 13 | 46% helix, 0% strand | Q9NJG9 |
| B | Probable histone-binding protein CAF1 | protein | 375 | 9% helix, 45% strand | Q24572 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.75 | 0.84 | 30 | SO4 |
| 2 | 71 | 0.41 | 0.80 | 17 | empty |
| 3 | 82 | 0.37 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2YB8 · Crystal structure of Nurf55 in complex with Su(z)12 · the same entry in another collection · chain B against B, TM-score 1.00
- Q24572 · AlphaFold monomer V2.0 prediction for chromatin assembly factor 1 P55 subunit (Q24572) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9NJG9 · AlphaFold monomer V2.0 prediction for polycomb protein SU(Z)12 (Q9NJG9) · a predicted model of the same protein · chain A against A, TM-score 0.64
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 Q9NJG9
- Every structure of UniProt Q24572
- Elsewhere: RCSB PDB 2YB8 · PDBe 2YB8 · UniProt Q9NJG9 · UniProt Q24572
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