Research workbench
Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide
Analyse Crystal structure of RBBP4 in complex with PRDM3 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
- 6BW3
- Type
- protein
- Length
- 763 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-binding protein RBBP4; MDS1 and EVI1 complex locus protein MDS1
- UniProt
- Q09028, Q13465
- Ligands
- UNX
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Histone-binding protein RBBP4 | protein | 369 | 8% helix, 45% strand | Q09028 |
| B, D | MDS1 and EVI1 complex locus protein MDS1 | protein | 10 | 0% helix, 0% strand | Q13465 |
| A | Histone-binding protein RBBP4 | protein | 374 | 9% helix, 45% strand | Q09028 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 12 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.75 | 0.82 | 55 | empty |
| 2 | 410 | 0.74 | 0.84 | 33 | empty |
| 3 | 295 | 0.63 | 0.80 | 46 | empty |
| 4 | 84 | 0.61 | 0.89 | 21 | empty |
| 5 | 143 | 0.59 | 0.84 | 29 | empty |
Interfaces
4 interfaces between chains.
- C–A · 873 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 738 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 698 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BW3 · Crystal structure of RBBP4 in complex with PRDM3 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
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 Q13465
- Elsewhere: RCSB PDB 6BW3 · PDBe 6BW3 · UniProt Q09028 · UniProt Q13465
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