Research workbench
Crystal structure of hepatocyte nuclear factor 4ALPHA in complex with DNA: diabetes gene product
Analyse Crystal structure of hepatocyte nuclear factor 4ALPHA in complex with DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CBB
- Type
- protein + DNA
- Length
- 196 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatocyte nuclear factor 4-alpha promoter element DNA; Hepatocyte nuclear factor…
- UniProt
- P41235
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Hepatocyte nuclear factor 4-alpha promoter element DNA | dna | 21 | — | — |
| D | Hepatocyte nuclear factor 4-alpha promoter element DNA | dna | 21 | — | — |
| A | Hepatocyte nuclear factor 4-alpha, DNA binding domain | protein | 76 | 34% helix, 8% strand | P41235 |
| B | Hepatocyte nuclear factor 4-alpha, DNA binding domain | protein | 78 | 32% helix, 8% strand | P41235 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.48 | 0.75 | 30 | empty |
| 2 | 160 | 0.45 | 0.76 | 16 | empty |
| 3 | 133 | 0.40 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 898 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- D–B · 478 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–B · 438 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–A · 437 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–A · 414 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 3CBB · Crystal Structure of Hepatocyte Nuclear Factor 4alpha in complex with DNA: Diabetes Gene… · the same entry in another collection · chain C against C, TM-score 1.00
- P41235 · AlphaFold monomer V2.0 prediction for hepatocyte nuclear factor 4-alpha (P41235) · 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 P41235
- Elsewhere: RCSB PDB 3CBB · PDBe 3CBB · UniProt P41235
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