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Crystal structure of FOXO1 dbd bound to DBE1 DNA

Analyse Crystal structure of FOXO1 dbd bound to DBE1 DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CO6
Type: protein + DNA
Length: 123 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*DTP*DGP*DGP*DTP*DTP*DTP*DGP*DTP*DTP*DTP*DAP*DCP*DCP*DTP*DTP*DG)- 3'); DNA…
UniProt: Q12778
Ligands: CA, CL
Pockets: 4 · best druggability 0.46

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'- D(DTPDGPDGPDTPDTPDTPDGPDTPDTPDTPDAPDCPDCPDTPDTPDG)- 3')	dna	16	—	—
B	DNA (5'- D(DCPDAPDAPDGPDGPDTPDAPDAPDAPDCPDAPDAPDAPDCPDCPDA)- 3')	dna	16	—	—
C	Forkhead box protein O1	protein	91	46% helix, 12% strand	Q12778

Ligands and binding sites

CA · Calcium ion · metal · chains C
CL · Chloride ion · ion

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

Pockets

4 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	156	0.46	0.77	18	CL
2	119	0.35	0.73	20	empty
3	99	0.32	0.73	15	empty
4	55	0.29	0.75	13	empty

Interfaces

3 interfaces between chains.

A–B · 708 Å² buried · 55 hydrogen bonds · nucleic-nucleic
A–C · 445 Å² buried · 9 hydrogen bonds · protein-nucleic
B–C · 405 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

3CO6 · Crystal Structure of FoxO1 DBD Bound to DBE1 DNA · the same entry in another collection · chain A against A, TM-score 1.00
Q12778 · AlphaFold monomer V2.0 prediction for forkhead box protein O1 (Q12778) · a predicted model of the same protein · chain C against A, TM-score 0.92

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 Q12778
Elsewhere: RCSB PDB 3CO6 · PDBe 3CO6 · UniProt Q12778

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