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MolNFT v1 · #153130 · protein + DNA

Crystal structure of the ATWRKY33 domain

6J4G · Probable wrky transcription factor 33: “Crystal structure of the ATWRKY33 domain”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #153130 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6J4G
Type
protein + DNA
Length
88 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Probable wrky transcription factor 33; DNA (5'-D(*AP*GP*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*C…
UniProt
Q8S8P5
Ligands
ZN

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 45% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BProbable wrky transcription factor 33protein580% helix, 45% strandQ8S8P5
CDNA (5'-D(*AP*GP*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*G)- 3')dna15——
DDNA (5'-D(*TP*CP*GP*CP*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*C)- 3')dna15——

Ligands and binding sites

  • ZN · Zinc ion · metal · chains B

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

Interfaces

3 interfaces between chains.

  • C–D · 654 Ų buried · 69 hydrogen bonds · nucleic-nucleic
  • B–D · 406 Ų buried · 7 hydrogen bonds · protein-nucleic
  • B–C · 289 Ų buried · 2 hydrogen bonds · protein-nucleic

Compared structures

  • 6J4G · Crystal structure of the AtWRKY33 domain · the same entry in another collection · chain B against B, TM-score 1.00
  • Q8S8P5 · AlphaFold monomer V2.0 prediction for probable wrky transcription factor 33 (Q8S8P5) · a predicted model of the same protein · chain B against A, TM-score 0.87

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