Research workbench
Multi-domain organization of the HNF4ALPHA nuclear receptor complex on DNA
Analyse Multi-domain organization of the HNF4ALPHA nuclear receptor complex on DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IQR
- Type
- protein + DNA
- Length
- 1,341 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte nuclear factor 4-alpha; DNA (5'- D(*GP*GP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*G…
- UniProt
- P41235, Q15596
- Ligands
- MYR, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 55% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatocyte nuclear factor 4-alpha | protein | 302 | 55% helix, 4% strand | P41235 |
| B | Hepatocyte nuclear factor 4-alpha | protein | 308 | 54% helix, 4% strand | P41235 |
| C, G | DNA (5'- D(*GP*GP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3') | dna | 20 | — | — |
| D, H | DNA (5'- D(*CP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*C)-3') | dna | 20 | — | — |
| E | Hepatocyte nuclear factor 4-alpha | protein | 303 | 58% helix, 4% strand | P41235 |
| F | Hepatocyte nuclear factor 4-alpha | protein | 314 | 54% helix, 4% strand | P41235 |
| I, K, L | Nuclear receptor coactivator 2 | protein | 8 | 63% helix, 0% strand | Q15596 |
| J | Nuclear receptor coactivator 2 | protein | 10 | 60% helix, 0% strand | Q15596 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 4 copies · chains A, B, E, F
- ZN · Zinc ion · metal · 8 copies · chains A, B, E, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.83 | 0.97 | 24 | MYR |
| 2 | 178 | 0.83 | 0.97 | 28 | MYR |
| 3 | 195 | 0.83 | 0.96 | 33 | MYR |
| 4 | 195 | 0.83 | 0.96 | 23 | MYR |
| 5 | 971 | 0.77 | 0.80 | 79 | empty |
Interfaces
17 interfaces between chains.
- A–B · 2077 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2018 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 850 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- G–H · 849 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- F–G · 546 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 4IQR · Multi-Domain Organization of the HNF4alpha Nuclear Receptor Complex on DNA · the same entry in another collection · chain L against L, TM-score 1.00
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 P41235
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 4IQR · PDBe 4IQR · UniProt P41235 · UniProt Q15596
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