Research workbench
Crystal structure of VAL1 B3 domain in complex with cognate DNA
Analyse Crystal structure of VAL1 B3 domain in complex with cognate DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FAS
- Type
- protein + DNA
- Length
- 268 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B3 domain-containing transcription repressor VAL1; DNA…
- UniProt
- Q8W4L5
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | B3 domain-containing transcription repressor VAL1 | protein | 110 | 15% helix, 48% strand | Q8W4L5 |
| C, E | DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3') | dna | 12 | — | — |
| D, F | DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3') | dna | 12 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.70 | 0.86 | 32 | empty |
| 2 | 51 | 0.39 | 0.82 | 14 | empty |
| 3 | 95 | 0.31 | 0.72 | 18 | empty |
Interfaces
7 interfaces between chains.
- A–B · 929 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 573 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- E–F · 567 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- B–E · 442 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 427 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 6FAS · Crystal structure of VAL1 B3 domain in complex with cognate DNA · 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 6FAS · PDBe 6FAS · UniProt Q8W4L5
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