MolNFT v1 · #138167 · protein
Crystal structure of a SUZ12-RBBP4-JARID2-AEBP2 heterotetrameric complex
5WAI · Histone-binding protein RBBP4: “Crystal structure of a SUZ12-RBBP4-JARID2-AEBP2 heterotetrameric complex”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.78). MolNFT v1 #138167 on GenesisL1: 3D structure, binding…
- PDB
- 5WAI
- Type
- protein
- Length
- 1,584 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-binding protein RBBP4; Polycomb protein SUZ12; Zinc finger protein AEBP2…
- UniProt
- Q09028, Q15022, Q6ZN18, U6DXQ8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-binding protein RBBP4 | protein | 397 | 11% helix, 42% strand | Q09028 |
| B | Polycomb protein SUZ12 | protein | 300 | 23% helix, 34% strand | Q15022 |
| C | Zinc finger protein AEBP2 | protein | 91 | 22% helix, 34% strand | Q6ZN18 |
| D, H | Jumonji, at-rich interactive domain 2 | protein | 15 | 60% helix, 7% strand | U6DXQ8 |
| E | Histone-binding protein RBBP4 | protein | 391 | 10% helix, 42% strand | Q09028 |
| F | Polycomb protein SUZ12 | protein | 289 | 23% helix, 37% strand | Q15022 |
| G | Zinc finger protein AEBP2 | protein | 86 | 12% helix, 36% strand | Q6ZN18 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.78 | 0.80 | 129 | empty |
| 2 | 488 | 0.76 | 0.84 | 38 | empty |
| 3 | 952 | 0.76 | 0.79 | 115 | empty |
| 4 | 453 | 0.75 | 0.84 | 33 | empty |
| 5 | 248 | 0.72 | 0.87 | 40 | empty |
Interfaces
13 interfaces between chains.
- A–B · 4995 Ų buried · 98 hydrogen bonds · protein-protein
- E–F · 4247 Ų buried · 93 hydrogen bonds · protein-protein
- B–C · 1263 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 1227 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1018 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5WAI · Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric Complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q09028 · AlphaFold monomer V2.0 prediction for histone-binding protein RBBP4 (Q09028) · a predicted model of the same protein · chain E against A, TM-score 0.99
- Q15022 · AlphaFold monomer V2.0 prediction for polycomb protein SUZ12 (Q15022) · a predicted model of the same protein · chain F against A, TM-score 0.98
- Q6ZN18 · AlphaFold monomer V2.0 prediction for zinc finger protein AEBP2 (Q6ZN18) · a predicted model of the same protein · chain G against A, TM-score 0.94
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 Q15022
- Every structure of UniProt Q6ZN18
- Every structure of UniProt U6DXQ8
- Elsewhere: RCSB PDB 5WAI · PDBe 5WAI · UniProt Q09028 · UniProt Q15022 · UniProt Q6ZN18 · UniProt U6DXQ8
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