MolNFT v1 · #138168 · protein
Crystal structure of a SUZ12-RBBP4 binary complex
5WAK · Histone-binding protein RBBP4: “Crystal structure of a SUZ12-RBBP4 binary complex”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.75). MolNFT v1 #138168 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5WAK
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-binding protein RBBP4; Polycomb protein SUZ12
- UniProt
- Q09028, Q15022
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-binding protein RBBP4 | protein | 392 | 9% helix, 42% strand | Q09028 |
| B | Polycomb protein SUZ12 | protein | 196 | 27% helix, 18% strand | Q15022 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.75 | 0.84 | 32 | empty |
| 2 | 229 | 0.70 | 0.86 | 32 | empty |
| 3 | 105 | 0.53 | 0.83 | 18 | empty |
| 4 | 213 | 0.51 | 0.76 | 22 | empty |
| 5 | 65 | 0.44 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4988 Ų buried · 95 hydrogen bonds · protein-protein
Compared structures
- 5WAK · Crystal Structure of a Suz12-Rbbp4 Binary Complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q09028 · AlphaFold monomer V2.0 prediction for histone-binding protein RBBP4 (Q09028) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q15022 · AlphaFold monomer V2.0 prediction for polycomb protein SUZ12 (Q15022) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 Q09028
- Every structure of UniProt Q15022
- Elsewhere: RCSB PDB 5WAK · PDBe 5WAK · UniProt Q09028 · UniProt Q15022
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