Research workbench
Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide
Analyse Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BW4
- Type
- protein
- Length
- 767 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-binding protein RBBP4; Pr domain zinc finger protein 16
- UniProt
- Q09028, Q9HAZ2
- Ligands
- UNX
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Histone-binding protein RBBP4 | protein | 370 | 9% helix, 46% strand | Q09028 |
| B, D | Pr domain zinc finger protein 16 | protein | 10 | 0% helix, 0% strand | Q9HAZ2 |
| A | Histone-binding protein RBBP4 | protein | 377 | 9% helix, 44% strand | Q09028 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 12 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.75 | 0.81 | 54 | empty |
| 2 | 436 | 0.74 | 0.84 | 31 | empty |
| 3 | 76 | 0.61 | 0.90 | 20 | empty |
| 4 | 269 | 0.60 | 0.79 | 41 | empty |
| 5 | 110 | 0.56 | 0.84 | 29 | empty |
Interfaces
4 interfaces between chains.
- C–A · 869 Ų buried · 10 hydrogen bonds · protein-protein
- C–B · 743 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 665 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BW4 · Crystal structure of RBBP4 in complex with PRDM16 N-terminal peptide · the same entry in another collection · chain C against C, TM-score 1.00
- Q09028 · AlphaFold monomer V2.0 prediction for histone-binding protein RBBP4 (Q09028) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q9HAZ2 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase PRDM16 (Q9HAZ2) · a predicted model of the same protein · chain B against A, TM-score 0.44
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 Q9HAZ2
- Elsewhere: RCSB PDB 6BW4 · PDBe 6BW4 · UniProt Q09028 · UniProt Q9HAZ2
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