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Structure of the human RBAP48 in complex with a macrocyclic peptide cyclized via a xylene linker attached to two cysteines
Analyse Structure of the human RBAP48 in complex with a macrocyclic peptide cyclized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZRD
- Type
- protein
- Length
- 828 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, SEZ, NH2
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-binding protein RBBP4 | protein | 411 | 11% helix, 41% strand | Q09028 |
| B | Histone-binding protein RBBP4 | protein | 389 | 12% helix, 43% strand | Q09028 |
| P, Q | Macrocyclic peptide based on residues 659-672 of the metastasis-associated protein MTA1 | protein | 14 | 43% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains P, Q
- SEZ · 1,3,5-trimethylbenzene · ligand · 2 copies · chains A, P, B, Q
- NH2 · Amino group · ion · 2 copies · chains P, 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 | 390 | 0.75 | 0.85 | 31 | empty |
| 2 | 570 | 0.74 | 0.82 | 46 | empty |
| 3 | 161 | 0.58 | 0.83 | 28 | empty |
| 4 | 210 | 0.53 | 0.78 | 38 | empty |
| 5 | 102 | 0.48 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1074 Ų buried · 14 hydrogen bonds · protein-protein
- A–P · 863 Ų buried · 15 hydrogen bonds · protein-protein
- B–Q · 858 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6ZRD · 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 0.99
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
- Elsewhere: RCSB PDB 6ZRD · PDBe 6ZRD · UniProt Q09028
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