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Structure of FOXG1 DNA binding domain bound to DBE2 DNA site

Analyse Structure of FOXG1 DNA binding domain bound to DBE2 DNA site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7CBY
Type: protein + DNA
Length: 132 residues
Chains: 3
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: P55316
Pockets: 3 · best druggability 0.41

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'-D(TPCPTPTPGPTPTPTPAPCPAPTPTPTPTPG)- 3')	dna	16	—	—
B	DNA (5'-D(CPAPAPAPAPTPGPTPAPAPAPCPAPAPGPA)- 3')	dna	16	—	—
C	Forkhead box protein G1	protein	100	45% helix, 15% strand	P55316

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.41	0.78	15	empty
2	97	0.33	0.74	13	empty
3	51	0.22	0.71	13	empty

Interfaces

3 interfaces between chains.

A–B · 710 Å² buried · 57 hydrogen bonds · nucleic-nucleic
A–C · 545 Å² buried · 11 hydrogen bonds · protein-nucleic
B–C · 447 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

7CBY · Structure of FOXG1 DNA binding domain bound to DBE2 DNA site · the same entry in another collection · chain A against A, TM-score 1.00
P55316 · AlphaFold monomer V2.0 prediction for forkhead box protein G1 (P55316) · a predicted model of the same protein · chain C 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 P55316
Elsewhere: RCSB PDB 7CBY · PDBe 7CBY · UniProt P55316

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