MolNFT v1 · #153279 · protein + DNA
Crystal structure of arabidopsis thaliana VAL1 in complex with flc DNA fragment
6J9A · B3 domain-containing transcription repressor VAL1: “Crystal structure of arabidopsis thaliana VAL1 in complex with flc DNA fragment”. X-ray diffraction, 2 pockets (best druggability 0.39). MolNFT v1 #153279 on GenesisL1: 3D…
- 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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