Research workbench
Complex of the C-terminal wrky domain of ATWRKY4 and a W-box DNA
Analyse Complex of the C-terminal wrky domain of ATWRKY4 and a W-box DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2LEX
- Type
- protein + DNA
- Length
- 83 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable wrky transcription factor 4; DNA (5'-D(*CP*G*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*…
- UniProt
- Q9XI90
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.29
Structure
solution nmr · 3 distinct chains · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable wrky transcription factor 4 | protein | 63 | 0% helix, 62% strand | Q9XI90 |
| B | DNA (5'-D(*CP*G*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*GP*C)- 3') | dna | 10 | — | — |
| C | DNA (5'-D(*GP*CP*GP*C*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*CP*G)- 3') | dna | 10 | — | — |
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.29 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 473 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- A–C · 348 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–B · 316 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 2LEX · Complex of the C-terminal WRKY domain of AtWRKY4 and a W-box DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XI90 · AlphaFold monomer V2.0 prediction for probable wrky transcription factor 4 (Q9XI90) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 Q9XI90
- Elsewhere: RCSB PDB 2LEX · PDBe 2LEX · UniProt Q9XI90
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