MolNFT v1 · #34121 · protein + DNA
Crystal structure of hnf-6ALPHA DNA-binding domain in complex with the ttr promoter
2D5V · 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3': “Crystal structure of hnf-6ALPHA DNA-binding domain in complex with the ttr promoter”. X-ray diffraction, 10 pockets (best druggability 0.66). MolNFT v1 #34121 on GenesisL1: 3D…
- PDB
- 2D5V
- Type
- protein + DNA
- Length
- 323 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3'…
- UniProt
- P70512
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3' | dna | 14 | — | — |
| D | 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3' | dna | 13 | — | — |
| F | 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3' | dna | 12 | — | — |
| A, B | Hepatocyte nuclear factor 6 | protein | 135 | 67% helix, 0% strand | P70512 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains D, A, E, F, B
- GOL · Glycerol · additive · 2 copies · chains F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.66 | 0.83 | 34 | GOL |
| 2 | 82 | 0.66 | 0.92 | 23 | empty |
| 3 | 207 | 0.54 | 0.78 | 26 | empty |
| 4 | 96 | 0.51 | 0.83 | 13 | ACT |
| 5 | 150 | 0.47 | 0.77 | 20 | empty |
Interfaces
10 interfaces between chains.
- E–B · 841 Ų buried · 26 hydrogen bonds · protein-nucleic
- D–A · 768 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–A · 748 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–B · 737 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 573 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Compared structures
- 2D5V · Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter · the same entry in another collection · chain E against E, TM-score 1.00
- P70512 · AlphaFold monomer V2.0 prediction for hepatocyte nuclear factor 6 (P70512) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P70512
- Elsewhere: RCSB PDB 2D5V · PDBe 2D5V · UniProt P70512
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