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Human TCF4 C-terminal bhlh domain in complex with 11-bp oligonucleotide containing E-box sequence

Analyse Human TCF4 C-terminal bhlh domain in complex with 11-bp oligonucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OD4
Type: protein + DNA
Length: 248 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription factor 4; DNA (5'-D(*TP*AP*CP*AP*CP*GP*TP*GP*TP*A)-3')
UniProt: P15884
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Transcription factor 4	protein	61	80% helix, 0% strand	P15884
G	Transcription factor 4	protein	53	79% helix, 0% strand	P15884
H	Transcription factor 4	protein	53	77% helix, 0% strand	P15884
X, W	DNA (5'-D(TPAPCPAPCPGPTPGPTPA)-3')	dna	10	—	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains X, W

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

Pockets

3 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	120	0.79	0.97	21	empty
2	684	0.70	0.77	53	empty
3	53	0.31	0.76	11	empty

Interfaces

11 interfaces between chains.

G–H · 1031 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 1023 Å² buried · 2 hydrogen bonds · protein-protein
X–W · 519 Å² buried · 42 hydrogen bonds · nucleic-nucleic
B–X · 430 Å² buried · 10 hydrogen bonds · protein-nucleic
A–W · 424 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

6OD4 · Human TCF4 C-terminal bHLH domain in Complex with 11-bp Oligonucleotide Containing E-box… · the same entry in another collection · chain W against W, TM-score 1.00
P15884 · AlphaFold monomer V2.0 prediction for transcription factor 4 (P15884) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 P15884
Elsewhere: RCSB PDB 6OD4 · PDBe 6OD4 · UniProt P15884

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