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The crystal structure of the second Z-DNA binding domain of human dai (ZBP1) in complex with Z-DNA
Analyse The crystal structure of the second Z-DNA binding domain of human dai (ZBP1) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EYI
- Type
- protein + DNA
- Length
- 144 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Z-DNA-binding protein 1; 5'-tcgcgcg-3'
- UniProt
- Q9H171
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Z-DNA-binding protein 1 | protein | 64 | 50% helix, 14% strand | Q9H171 |
| B | Z-DNA-binding protein 1 | protein | 67 | 48% helix, 13% strand | Q9H171 |
| C | 5'-tcgcgcg-3' | dna | 6 | — | — |
| D | 5'-tcgcgcg-3' | dna | 7 | — | — |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.49 | 0.79 | 17 | empty |
| 2 | 71 | 0.38 | 0.79 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–C · 378 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 330 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- B–D · 281 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 58 Ų buried · 0 hydrogen bonds · protein-nucleic
- B–C · 38 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 3EYI · The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H171 · AlphaFold monomer V2.0 prediction for Z-DNA-binding protein 1 (Q9H171) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q9H171
- Elsewhere: RCSB PDB 3EYI · PDBe 3EYI · UniProt Q9H171
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