Research workbench
Crystal structure of FOXA2 DNA binding domain bound to a full consensus DNA site
Analyse Crystal structure of FOXA2 DNA binding domain bound to a full consensus DNA site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X07
- Type
- protein + DNA
- Length
- 464 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)- 3'); DNA…
- UniProt
- Q9Y261
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, G, J | DNA (5'-D(*TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)- 3') | dna | 16 | — | — |
| E, B, H, K | DNA (5'-D(*CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)- 3') | dna | 16 | — | — |
| F, L | Hepatocyte nuclear factor 3-beta | protein | 85 | 46% helix, 12% strand | Q9Y261 |
| C | Hepatocyte nuclear factor 3-beta | protein | 84 | 48% helix, 11% strand | Q9Y261 |
| I | Hepatocyte nuclear factor 3-beta | protein | 82 | 48% helix, 13% strand | Q9Y261 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.63 | 0.78 | 39 | empty |
| 2 | 451 | 0.61 | 0.76 | 41 | empty |
| 3 | 340 | 0.58 | 0.77 | 36 | empty |
| 4 | 340 | 0.57 | 0.76 | 28 | empty |
| 5 | 134 | 0.42 | 0.76 | 18 | empty |
Interfaces
21 interfaces between chains.
- J–K · 717 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- A–B · 715 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- D–E · 704 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- G–H · 699 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- K–L · 545 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 5X07 · Crystal structure of FOXA2 DNA binding domain bound to a full consensus DNA site · 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 Q9Y261
- Elsewhere: RCSB PDB 5X07 · PDBe 5X07 · UniProt Q9Y261
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