Research workbench
Crystal structure of BEND3-BEN4-DNA complex
Analyse Crystal structure of BEND3-BEN4-DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W27
- Type
- protein + DNA
- Length
- 137 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*CP*GP*CP*AP*GP*C)-3'); DNA…
- UniProt
- Q5T5X7
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*CP*GP*CP*AP*GP*C)-3') | dna | 13 | — | — |
| B | DNA (5'-D(P*GP*GP*CP*TP*GP*CP*GP*TP*GP*GP*GP*TP*C)-3') | dna | 13 | — | — |
| C | Ben domain-containing protein 3 | protein | 111 | 59% helix, 4% strand | Q5T5X7 |
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.57 | 0.80 | 27 | empty |
| 2 | 145 | 0.55 | 0.82 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–C · 555 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 555 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–C · 481 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (engineered).
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 Q5T5X7
- Elsewhere: RCSB PDB 7W27 · PDBe 7W27 · UniProt Q5T5X7
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