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Structure of BSG25A binding with DNA
Analyse Structure of BSG25A binding with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X0G
- Type
- protein + DNA
- Length
- 486 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blastoderm-specific gene 25A; DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3')
- UniProt
- Q9VR17
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Blastoderm-specific gene 25A | protein | 108 | 54% helix, 9% strand | Q9VR17 |
| B, C | Blastoderm-specific gene 25A | protein | 109 | 52% helix, 9% strand | Q9VR17 |
| E, F, G, H | DNA (5'-D(*GP*TP*TP*CP*CP*AP*AP*TP*TP*GP*GP*AP*A)-3') | dna | 13 | — | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.86 | 0.87 | 70 | empty |
| 2 | 565 | 0.83 | 0.89 | 47 | empty |
| 3 | 101 | 0.43 | 0.79 | 19 | empty |
| 4 | 120 | 0.42 | 0.77 | 16 | empty |
| 5 | 50 | 0.41 | 0.83 | 12 | empty |
Interfaces
21 interfaces between chains.
- B–F · 665 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–G · 655 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–H · 623 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–E · 606 Ų buried · 12 hydrogen bonds · protein-nucleic
- G–H · 547 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
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 Q9VR17
- Elsewhere: RCSB PDB 4X0G · PDBe 4X0G · UniProt Q9VR17
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