Research workbench
Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with double-stranded DNA contaning CACACGTGTG
Analyse Crystal structure of MBP-fused BIL1/BZR1 (21-90) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VN3
- Type
- protein + DNA
- Length
- 1,806 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Arabidopsis thaliana; Serratia sp. (strain FS14); SYNTHETIC CONSTRUCT
- Molecule
- Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1; DNA…
- UniProt
- A0A4P1LXE0, Q8S307
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 1.94 · 3 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1 | protein | 437 | 48% helix, 19% strand | A0A4P1LXE0, Q8S307 |
| D, B | Maltodextrin-binding protein,Protein BRASSINAZOLE-RESISTANT 1 | protein | 436 | 47% helix, 19% strand | A0A4P1LXE0, Q8S307 |
| G, H, E, F | DNA (5'-D(*TP*TP*CP*AP*CP*AP*CP*GP*TP*GP*TP*GP*AP*AP*A)-3') | dna | 15 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains C, D, H, G, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.86 | 0.95 | 28 | EDO |
| 2 | 595 | 0.82 | 0.87 | 41 | empty |
| 3 | 642 | 0.81 | 0.86 | 68 | GLC, EDO |
| 4 | 690 | 0.81 | 0.85 | 80 | GLC |
| 5 | 652 | 0.77 | 0.83 | 66 | empty |
Interfaces
14 interfaces between chains.
- C–D · 1860 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1731 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 675 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- G–H · 667 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- D–A · 572 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- Q8S307 · AlphaFold monomer V2.0 prediction for protein brassinazole-resistant 1 (Q8S307) · a predicted model of the same protein · chain B against A, TM-score 0.19
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 A0A4P1LXE0
- Every structure of UniProt Q8S307
- Elsewhere: RCSB PDB 7VN3 · PDBe 7VN3 · UniProt A0A4P1LXE0 · UniProt Q8S307
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