Research workbench
Crystal structure of FOXC2 dbd bound to DBE2 DNA
Analyse Crystal structure of FOXC2 dbd bound to DBE2 DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AKO
- Type
- protein + DNA
- Length
- 129 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)- 3'); DNA…
- UniProt
- Q99958
- Ligands
- MG
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(CP*AP*AP*AP*AP*TP*GP*TP*AP*AP*AP*CP*AP*AP*GP*A)- 3') | dna | 16 | — | — |
| B | DNA (5'-D(TP*CP*TP*TP*GP*TP*TP*TP*AP*CP*AP*TP*TP*TP*TP*G)- 3') | dna | 16 | — | — |
| C | Forkhead box protein C2 | protein | 97 | 44% helix, 11% strand | Q99958 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.53 | 0.77 | 26 | empty |
| 2 | 112 | 0.34 | 0.73 | 13 | empty |
| 3 | 74 | 0.27 | 0.72 | 17 | empty |
| 4 | 51 | 0.27 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 715 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- B–C · 557 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 452 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
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 Q99958
- Elsewhere: RCSB PDB 6AKO · PDBe 6AKO · UniProt Q99958
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