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MolNFT v1 · #28977 · protein + DNA

Solution NMR structure of the gaga FACTOR/DNA complex, regularized mean structure

1YUI · DNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3'): “Solution NMR structure of the gaga FACTOR/DNA complex, regularized mean structure”. Solution nmr, 1 ligand (ZN). MolNFT v1 #28977 on GenesisL1: 3D structure, binding sites and…

PDB
1YUI
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 · 28% helix, 7% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BDNA (5'-D(*GP*CP*CP*GP*AP*GP*AP*GP*TP*AP*C)-3')dna11——
CDNA (5'-D(*GP*TP*AP*CP*TP*CP*TP*CP*GP*GP*C)-3')dna11——
AGaga-factorprotein5428% helix, 7% strandQ08605

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 · 832 Ų buried · 16 hydrogen bonds · protein-nucleic
  • B–C · 543 Ų buried · 40 hydrogen bonds · nucleic-nucleic
  • C–A · 498 Ų buried · 6 hydrogen bonds · protein-nucleic

Compared structures

  • 1YUI · Solution NMR structure of the gaga FACTOR/DNA complex, regularized mean structure · the same entry in another collection · chain B against B, 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 0.53

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