Research workbench
Crystal structure of arabidopsis thaliana VAL1 in complex with flc DNA fragment
Analyse Crystal structure of arabidopsis thaliana VAL1 in complex with flc DNA fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J9A
- Type
- protein + DNA
- Length
- 136 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B3 domain-containing transcription repressor VAL1; DNA…
- UniProt
- Q8W4L5
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B3 domain-containing transcription repressor VAL1 | protein | 106 | 15% helix, 43% strand | Q8W4L5 |
| B | DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*TP*G)- 3') | dna | 15 | — | — |
| C | DNA (5'-D(*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*C)- 3') | dna | 15 | — | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.39 | 0.77 | 17 | empty |
| 2 | 83 | 0.33 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 676 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- A–C · 440 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 359 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 6J9A · Crystal structure of Arabidopsis thaliana VAL1 in complex with FLC DNA fragment · the same entry in another collection · chain A against A, TM-score 1.00
- Q8W4L5 · AlphaFold monomer V2.0 prediction for B3 domain-containing transcription repressor VAL1… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8W4L5
- Elsewhere: RCSB PDB 6J9A · PDBe 6J9A · UniProt Q8W4L5
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