Research workbench
The crystal structure of human forkhead box protein a in complex with DNA 2
Analyse The crystal structure of human forkhead box protein a in complex with DNA 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VOX
- Type
- protein + DNA
- Length
- 402 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3'); DNA (5'…
- UniProt
- P55317
- Ligands
- MG
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F | DNA (5'- D(P*TP*CP*GP*AP*TP*AP*AP*TP*AP*AP*AP*TP*AP*TP*TP*T)-3') | dna | 16 | — | — |
| E, G | DNA (5'- D(P*AP*AP*AP*TP*AP*TP*TP*TP*AP*TP*TP*AP*TP*CP*GP*A)-3') | dna | 16 | — | — |
| A, C, H | Hepatocyte nuclear factor 3-alpha | protein | 85 | 49% helix, 12% strand | P55317 |
| B | Hepatocyte nuclear factor 3-alpha | protein | 83 | 48% helix, 12% strand | P55317 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.66 | 0.77 | 63 | empty |
| 2 | 476 | 0.64 | 0.77 | 61 | empty |
| 3 | 197 | 0.53 | 0.78 | 31 | empty |
| 4 | 50 | 0.45 | 0.85 | 14 | empty |
| 5 | 177 | 0.44 | 0.75 | 20 | empty |
Interfaces
19 interfaces between chains.
- F–G · 727 Ų buried · 70 hydrogen bonds · nucleic-nucleic
- D–E · 724 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- G–H · 533 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–A · 528 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–C · 512 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7VOX · The crystal structure of human forkhead box protein A in complex with DNA 2 · the same entry in another collection · chain H against H, TM-score 1.00
- P55317 · AlphaFold monomer V2.0 prediction for hepatocyte nuclear factor 3-alpha (P55317) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P55317
- Elsewhere: RCSB PDB 7VOX · PDBe 7VOX · UniProt P55317
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