MolNFT v1 · #147933 · protein + DNA

Structure of CDX2-DNA(CAA)

6ES2 · DNA (5'- D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*CP*CP*TP…: “Structure of CDX2-DNA(CAA)”. X-ray diffraction, 2 pockets (best druggability 0.69). MolNFT v1 #147933 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ES2
Type: protein + DNA
Length: 212 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*TP*TP*GP*CP*CP*TP*CP*C)-3'); Homeobox protein…
UniProt: Q99626
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (5'- D(PTPTPGPTPGPTPTPTPTPAPTPTPGPCPCPTPCPC)-3')	dna	18	—	—
K	Homeobox protein cdx-2	protein	70	73% helix, 0% strand	Q99626
L	Homeobox protein cdx-2	protein	70	73% helix, 0% strand	Q99626
D, E	DNA (5'- D(PGPGPAPGPGPCPAPAPTPAPAPAPAPCPAPCPAPA)-3')	dna	18	—	—

Pockets

2 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	556	0.69	0.79	48	empty
2	536	0.68	0.79	49	empty

Interfaces

9 interfaces between chains.

B–E · 802 Å² buried · 75 hydrogen bonds · nucleic-nucleic
A–D · 798 Å² buried · 73 hydrogen bonds · nucleic-nucleic
K–L · 708 Å² buried · 5 hydrogen bonds · protein-protein
L–E · 551 Å² buried · 9 hydrogen bonds · protein-nucleic
K–D · 544 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

6ES2 · Structure of CDX2-DNA(CAA) · 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 K 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 6ES2 · PDBe 6ES2 · UniProt Q99626

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.