MolNFT v1 · #190266 · protein + DNA
Crystal structure of arabidopsis transcriptional factor WRINKLED1 with dsdna
7WQ5 · Ethylene-responsive transcription factor WRI1: “Crystal structure of arabidopsis transcriptional factor WRINKLED1 with dsdna”. X-ray diffraction, 1 ligand (NH4), 9 pockets (best druggability 0.67). MolNFT v1 #190266 on GenesisL1: 3D…
- PDB
- 7WQ5
- Type
- protein + DNA
- Length
- 426 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ethylene-responsive transcription factor WRI1; DNA (5'…
- UniProt
- Q6X5Y6
- Ligands
- NH4
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ethylene-responsive transcription factor WRI1 | protein | 172 | 34% helix, 26% strand | Q6X5Y6 |
| B | Ethylene-responsive transcription factor WRI1 | protein | 158 | 33% helix, 26% strand | Q6X5Y6 |
| F, D | DNA (5'- D(P*GP*TP*GP*GP*AP*CP*GP*AP*TP*GP*AP*AP*AP*CP*CP*GP*AP*GP*GP*AP*AP*GP *TP*A)-3') | dna | 24 | — | — |
| C, E | DNA (5'- D(P*TP*AP*CP*TP*TP*CP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*TP*CP*GP*TP*CP*CP *AP*C)-3') | dna | 24 | — | — |
Ligands and binding sites
- NH4 · Ammonium ion · ion · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.67 | 0.76 | 77 | empty |
| 2 | 316 | 0.59 | 0.78 | 30 | empty |
| 3 | 120 | 0.52 | 0.82 | 18 | empty |
| 4 | 104 | 0.44 | 0.79 | 16 | empty |
| 5 | 110 | 0.41 | 0.77 | 15 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1288 Ų buried · 27 hydrogen bonds · protein-nucleic
- B–E · 1154 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–D · 1067 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- F–E · 1060 Ų buried · 81 hydrogen bonds · nucleic-nucleic
- A–D · 904 Ų buried · 17 hydrogen bonds · protein-nucleic
Compared structures
- 7WQ5 · Crystal structure of Arabidopsis transcriptional factor WRINKLED1 with dsDNA · the same entry in another collection · chain E against E, TM-score 1.00
- Q6X5Y6 · AlphaFold monomer V2.0 prediction for ethylene-responsive transcription factor WRI1… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q6X5Y6
- Elsewhere: RCSB PDB 7WQ5 · PDBe 7WQ5 · UniProt Q6X5Y6
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