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Crystal structure of the ATWRKY2 domain

Analyse Crystal structure of the ATWRKY2 domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6J4F
Type: protein + DNA
Length: 186 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable wrky transcription factor 2; DNA (5'-D(*AP*GP*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP…
UniProt: Q9FG77
Ligands: ZN
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, F	Probable wrky transcription factor 2	protein	63	0% helix, 43% strand	Q9FG77
C, G	DNA (5'-D(APGPCPCPTPTPTPGPAPCPCPAPGPCP*G)- 3')	dna	15	—	—
D, H	DNA (5'-D(TPCPGPCPTPGPGPTPCPAPAPAPGPGP*C)- 3')	dna	15	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains B, F

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

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	160	0.52	0.79	25	empty
2	108	0.42	0.77	17	empty
3	74	0.32	0.75	13	empty
4	71	0.30	0.74	19	empty

Interfaces

7 interfaces between chains.

G–H · 662 Å² buried · 62 hydrogen bonds · nucleic-nucleic
C–D · 648 Å² buried · 62 hydrogen bonds · nucleic-nucleic
B–F · 608 Å² buried · 11 hydrogen bonds · protein-protein
F–H · 405 Å² buried · 11 hydrogen bonds · protein-nucleic
B–D · 389 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

6J4F · Crystal structure of the AtWRKY2 domain · the same entry in another collection · chain D against D, TM-score 1.00
Q9FG77 · AlphaFold monomer V2.0 prediction for probable wrky transcription factor 2 (Q9FG77) · a predicted model of the same protein · chain B against A, TM-score 0.85

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 Q9FG77
Elsewhere: RCSB PDB 6J4F · PDBe 6J4F · UniProt Q9FG77

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