Research workbench

Rice WRKY/DNA complex

Analyse Rice WRKY/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IR8
Type: protein + DNA
Length: 97 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: OSWRKY45; DNA (5'-D(P*GP*AP*TP*AP*TP*TP*TP*GP*AP*CP*CP*GP*GP*A)-3'); DNA…
UniProt: B9FNW2
Ligands: ZN
Pockets: 1 · best druggability 0.36

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	OSWRKY45	protein	69	0% helix, 36% strand	B9FNW2
B	DNA (5'-D(PGPAPTPAPTPTPTPGPAPCPCPGPGPA)-3')	dna	14	—	—
C	DNA (5'-D(PTPCPCPGPGPTPCPAPAPAPTPAPTPC)-3')	dna	14	—	—

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.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.36	0.76	14	empty

Interfaces

3 interfaces between chains.

B–C · 600 Å² buried · 56 hydrogen bonds · nucleic-nucleic
A–C · 387 Å² buried · 8 hydrogen bonds · protein-nucleic
A–B · 304 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6IR8 · Rice WRKY/DNA complex · the same entry in another collection · chain A against A, TM-score 1.00

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 B9FNW2
Elsewhere: RCSB PDB 6IR8 · PDBe 6IR8 · UniProt B9FNW2

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