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Crystal structure of FOXO1 dbd bound to ire DNA

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

PDB: 3COA
Type: protein + DNA
Length: 237 residues
Chains: 6
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*DTP*DGP*DCP*DTP*DTP*DG)- 3'); DNA…
UniProt: Q12778
Ligands: CA
Pockets: 6 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	DNA (5'- D(DTPDGPDGPDTPDTPDTPDGPDTPDTPDTPDTPDGPDCPDTPDTPDG)- 3')	dna	16	—	—
B, E	DNA (5'- D(DCPDAPDAPDGPDCPDAPDAPDAPDAPDCPDAPDAPDAPDCPDCPDA)- 3')	dna	16	—	—
C	Forkhead box protein O1	protein	86	48% helix, 13% strand	Q12778
F	Forkhead box protein O1	protein	87	48% helix, 13% strand	Q12778

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains C, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	835	0.67	0.75	72	empty
2	106	0.35	0.74	18	empty
3	91	0.33	0.74	14	empty
4	56	0.31	0.77	15	empty
5	90	0.31	0.73	16	empty

Interfaces

7 interfaces between chains.

D–E · 709 Å² buried · 58 hydrogen bonds · nucleic-nucleic
A–B · 705 Å² buried · 52 hydrogen bonds · nucleic-nucleic
D–F · 450 Å² buried · 9 hydrogen bonds · protein-nucleic
A–C · 439 Å² buried · 7 hydrogen bonds · protein-nucleic
E–F · 411 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

3COA · Crystal Structure of FoxO1 DBD Bound to IRE DNA · the same entry in another collection · chain F against F, 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 0.94

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 3COA · PDBe 3COA · UniProt Q12778

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