MolNFT v1 · #137590 · protein
Crystal structure of RBBP4 bound to BCL11A peptide
5VTB · Histone-binding protein RBBP4: “Crystal structure of RBBP4 bound to BCL11A peptide”. X-ray diffraction, 2 pockets (best druggability 0.77). MolNFT v1 #137590 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VTB
- Type
- protein
- Length
- 363 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-binding protein RBBP4; B-cell LYMPHOMA/LEUKEMIA 11A
- UniProt
- Q09028, Q9H165
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-binding protein RBBP4 | protein | 349 | 5% helix, 49% strand | Q09028 |
| B | B-cell LYMPHOMA/LEUKEMIA 11A | protein | 14 | 0% helix, 0% strand | Q9H165 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.77 | 0.85 | 32 | empty |
| 2 | 52 | 0.59 | 0.91 | 14 | GOL |
Interfaces
1 interface between chains.
- A–B · 883 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5VTB · Crystal structure of RBBP4 bound to BCL11a peptide · 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 0.99
- Q9H165 · AlphaFold monomer V2.0 prediction for B-cell LYMPHOMA/LEUKEMIA 11A (Q9H165) · a predicted model of the same protein · chain B against A, TM-score 0.24
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 Q9H165
- Elsewhere: RCSB PDB 5VTB · PDBe 5VTB · UniProt Q09028 · UniProt Q9H165
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