MolNFT v1 · #140158 · protein
Crystal structure of RBBP4 bound to AEBP2 rrk motif
5Y1U · Histone-binding protein RBBP4: “Crystal structure of RBBP4 bound to AEBP2 rrk motif”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.79). MolNFT v1 #140158 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5Y1U
- Type
- protein
- Length
- 777 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-binding protein RBBP4; Zinc finger protein AEBP2
- UniProt
- Q09028, Q6ZN18
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-binding protein RBBP4 | protein | 383 | 9% helix, 44% strand | Q09028 |
| B | Histone-binding protein RBBP4 | protein | 384 | 11% helix, 44% strand | Q09028 |
| C, D | Zinc finger protein AEBP2 | protein | 5 | 0% helix, 0% strand | Q6ZN18 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.79 | 0.81 | 115 | empty |
| 2 | 411 | 0.74 | 0.84 | 33 | empty |
| 3 | 117 | 0.60 | 0.85 | 25 | SO4 |
| 4 | 81 | 0.57 | 0.87 | 21 | SO4 |
| 5 | 218 | 0.47 | 0.74 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–B · 850 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 480 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 427 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Y1U · Crystal structure of RBBP4 bound to AEBP2 RRK motif · the same entry in another collection · chain D against D, 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
- Q6ZN18 · AlphaFold monomer V2.0 prediction for zinc finger protein AEBP2 (Q6ZN18) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 Q6ZN18
- Elsewhere: RCSB PDB 5Y1U · PDBe 5Y1U · UniProt Q09028 · UniProt Q6ZN18
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