MolNFT v1 · #172103 · protein
Structure of the human RBAP48 in complex with a macrocyclic peptide cyclized via a xylene linker attached to two cysteines
6ZRC · Histone-binding protein RBBP4: “Structure of the human RBAP48 in complex with a macrocyclic peptide cyclized via a xylene linker attached to…”. X-ray diffraction, 3 ligands (ACE, PXY, NH2), 9 pockets (best druggability 0.85). MolNFT…
- PDB
- 6ZRC
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-binding protein RBBP4; Macrocyclic peptide based on residues 659-672 of the…
- UniProt
- Q09028
- Ligands
- ACE, PXY, NH2
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-binding protein RBBP4 | protein | 381 | 9% helix, 43% strand | Q09028 |
| P, Q | Macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1 | protein | 14 | 29% helix, 0% strand | — |
| B | Histone-binding protein RBBP4 | protein | 381 | 9% helix, 42% strand | Q09028 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, P, B, Q
- PXY · Para-xylene · ligand · 2 copies · chains A, P, B, Q
- NH2 · Amino group · ion · 2 copies · chains P, B, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.85 | 0.90 | 55 | PXY |
| 2 | 416 | 0.73 | 0.84 | 31 | empty |
| 3 | 391 | 0.58 | 0.75 | 47 | empty |
| 4 | 220 | 0.54 | 0.78 | 34 | ACE |
| 5 | 179 | 0.49 | 0.76 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–P · 883 Ų buried · 13 hydrogen bonds · protein-protein
- Q–B · 870 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 527 Ų buried · 3 hydrogen bonds · protein-protein
- P–B · 345 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6ZRC · Structure of the human RBAP48 in complex with a macrocyclic peptide cyclized via a xylene… · 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 B against A, TM-score 0.96
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
- Elsewhere: RCSB PDB 6ZRC · PDBe 6ZRC · UniProt Q09028
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