Research workbench

Homeobox transcription factor CDX2 bound to methylated DNA

Analyse Homeobox transcription factor CDX2 bound to methylated DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LTY
Type: protein + DNA
Length: 213 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM) P*GP*AP*CP*CP*TP*CP*C)-3'); Homeobox…
UniProt: Q99626
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'-D(PTPTPGPTPGPTPTPTPTPAP(5CM) PGPAPCPCPTPCPC)-3')	dna	18	—	—
K	Homeobox protein cdx-2	protein	71	73% helix, 0% strand	Q99626
M	Homeobox protein cdx-2	protein	70	74% helix, 0% strand	Q99626
F, E	DNA (5'-D(PGPGPAPGPGPTP(5CM) PGPTPAPAPAPAPCPAPCPAPA)-3')	dna	18	—	—

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	655	0.72	0.79	52	empty
2	683	0.71	0.78	60	empty
3	59	0.34	0.77	13	empty
4	59	0.33	0.77	11	empty

Interfaces

9 interfaces between chains.

A–F · 788 Å² buried · 68 hydrogen bonds · nucleic-nucleic
B–E · 777 Å² buried · 63 hydrogen bonds · nucleic-nucleic
K–M · 749 Å² buried · 4 hydrogen bonds · protein-protein
A–K · 588 Å² buried · 20 hydrogen bonds · protein-nucleic
B–M · 565 Å² buried · 19 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

5LTY · Homeobox transcription factor CDX2 bound to methylated DNA · the same entry in another collection · chain E against E, TM-score 1.00
Q99626 · AlphaFold monomer V2.0 prediction for homeobox protein cdx-2 (Q99626) · a predicted model of the same protein · chain M 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 Q99626
Elsewhere: RCSB PDB 5LTY · PDBe 5LTY · UniProt Q99626

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