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MolNFT v1 · #126838 · protein + DNA

Crystal structure of SMAD4-MH1 bound to the ggcgc site.

5MEY · MH1 domain of human SMAD4: “Crystal structure of SMAD4-MH1 bound to the ggcgc site.”. X-ray diffraction, 3 ligands (CA, ZN, CL). MolNFT v1 #126838 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
5MEY
Type
protein + DNA
Length
142 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
MH1 domain of human SMAD4; DNA (5'- D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP…
UniProt
Q13485
Ligands
CA, ZN, CL

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AMH1 domain of human SMAD4protein12441% helix, 15% strandQ13485
DDNA (5'- D(P*AP*TP*GP*CP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*GP*CP*AP*T)-3')dna18——

Ligands and binding sites

  • CA · Calcium ion · metal · 5 copies · chains D
  • ZN · Zinc ion · metal · chains A
  • CL · Chloride ion · ion · 4 copies · chains A
  • PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
  • EDO · 1,2-ethanediol · additive · chains D

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

Interfaces

1 interface between chains.

  • A–D · 332 Ų buried · 9 hydrogen bonds · protein-nucleic

Compared structures

  • 5MEY · Crystal structure of Smad4-MH1 bound to the GGCGC site. · the same entry in another collection · chain A against A, TM-score 1.00
  • Q13485 · AlphaFold monomer V2.0 prediction for mothers against decapentaplegic homolog 4 (Q13485) · a predicted model of the same protein · chain A against A, TM-score 0.99

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