Research workbench
Crystal structure of mbp-fused BIL1/BZR1 in complex with double- stranded DNA
Analyse Crystal structure of mbp-fused BIL1/BZR1 in complex with double- stranded DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZD4
- Type
- protein + DNA
- Length
- 1,778 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,PROTEIN brassinazole- resistant 1; DNA…
- UniProt
- P0AEY0, Q8S307
- Ligands
- GLC
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Maltose-binding periplasmic PROTEIN,PROTEIN brassinazole- resistant 1 | protein | 436 | 47% helix, 19% strand | P0AEY0, Q8S307 |
| D | Maltose-binding periplasmic PROTEIN,PROTEIN brassinazole- resistant 1 | protein | 411 | 47% helix, 18% strand | P0AEY0, 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 | — | — |
| B | Maltose-binding periplasmic PROTEIN,PROTEIN brassinazole- resistant 1 | protein | 435 | 47% helix, 19% strand | P0AEY0, Q8S307 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains C, D, A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains C, H, D, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.86 | 0.95 | 26 | empty |
| 2 | 532 | 0.83 | 0.90 | 43 | EDO |
| 3 | 656 | 0.81 | 0.86 | 70 | GLC |
| 4 | 723 | 0.81 | 0.85 | 73 | GLC |
| 5 | 1108 | 0.81 | 0.82 | 86 | GLC |
Interfaces
14 interfaces between chains.
- A–B · 1744 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1716 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 677 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- G–H · 669 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- B–F · 549 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5ZD4 · Crystal structure of MBP-fused BIL1/BZR1 in complex with double-stranded DNA · the same entry in another collection · chain F against F, TM-score 1.00
- 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 P0AEY0
- Every structure of UniProt Q8S307
- Elsewhere: RCSB PDB 5ZD4 · PDBe 5ZD4 · UniProt P0AEY0 · UniProt Q8S307
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