Research workbench
Crystal structure of the human FOXN3 DNA binding domain in complex with a forkhead-like (fhl) DNA sequence
Analyse Crystal structure of the human FOXN3 DNA binding domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NCM
- Type
- protein + DNA
- Length
- 210 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Forkhead box protein N3; DNA (5'-D(*AP*TP*AP*GP*CP*GP*TP*CP*TP*TP*AP*GP*CP*AP*TP*G)- 3')…
- UniProt
- O00409
- Ligands
- MG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Forkhead box protein N3 | protein | 91 | 55% helix, 11% strand | O00409 |
| C | DNA (5'-D(*AP*TP*AP*GP*CP*GP*TP*CP*TP*TP*AP*GP*CP*AP*TP*G)- 3') | dna | 16 | — | — |
| D | DNA (5'-D(*TP*CP*AP*TP*GP*CP*TP*AP*AP*GP*AP*CP*GP*CP*TP*A)- 3') | dna | 16 | — | — |
| B | Forkhead box protein N3 | protein | 87 | 52% helix, 11% strand | O00409 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.74 | 0.79 | 66 | empty |
| 2 | 160 | 0.46 | 0.76 | 26 | empty |
| 3 | 51 | 0.43 | 0.83 | 11 | empty |
Interfaces
6 interfaces between chains.
- C–D · 710 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–C · 464 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 393 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–B · 313 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–B · 175 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 6NCM · Crystal structure of the human FOXN3 DNA binding domain in complex with a forkhead-like… · the same entry in another collection · chain A against A, TM-score 1.00
- O00409 · AlphaFold monomer V2.0 prediction for forkhead box protein N3 (O00409) · a predicted model of the same protein · chain B 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 O00409
- Elsewhere: RCSB PDB 6NCM · PDBe 6NCM · UniProt O00409
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.