MolNFT v1 · #28978 · protein + DNA

Solution NMR structure of the gaga FACTOR/DNA complex, 50 structures

1YUJ · DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3'): “Solution NMR structure of the gaga FACTOR/DNA complex, 50 structures”. Solution nmr, 1 ligand (ZN). MolNFT v1 #28978 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1YUJ
Type: protein + DNA
Length: 76 residues
Chains: 3
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3'); DNA…
UniProt: Q08605
Ligands: ZN

Structure

solution nmr · 3 distinct chains · 20% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA (5'-D(GPCPCPGPAPGPAPGPTPAP*C)-3')	dna	11	—	—
C	DNA (5'-D(GPTPAPCPTPCPTPCPGPGP*C)-3')	dna	11	—	—
A	Gaga-factor	protein	54	20% helix, 7% strand	Q08605

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Interfaces

3 interfaces between chains.

B–A · 820 Å² buried · 12 hydrogen bonds · protein-nucleic
B–C · 538 Å² buried · 43 hydrogen bonds · nucleic-nucleic
C–A · 493 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

1YUJ · Solution NMR structure of the gaga FACTOR/DNA complex, 50 structures · the same entry in another collection · chain A against A, TM-score 1.00
Q08605 · AlphaFold monomer V2.0 prediction for transcription factor gaga (Q08605) · a predicted model of the same protein · chain A against A, TM-score 0.52

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 Q08605
Elsewhere: RCSB PDB 1YUJ · PDBe 1YUJ · UniProt Q08605

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