Research workbench
Zinc finger-DNA recognition: crystal structure of a ZIF268- DNA complex at 2.1 ångströms
Analyse Zinc finger-DNA recognition: crystal structure of a ZIF268- DNA complex at 2.1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZAA
- Type
- protein + DNA
- Length
- 107 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3'); DNA…
- UniProt
- P08046
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*CP*GP*T)-3') | dna | 11 | — | — |
| B | DNA (5'-D(*TP*AP*CP*GP*CP*CP*CP*AP*CP*GP*C)-3') | dna | 11 | — | — |
| C | Protein (ZIF268) | protein | 85 | 41% helix, 14% strand | P08046 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 97 | 0.61 | 0.89 | 18 | empty |
| 2 | 58 | 0.58 | 0.91 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 971 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 535 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 485 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Compared structures
- 1ZAA · Zinc finger-DNA recognition: crystal structure of a ZIF268-DNA complex at 2.1 ångströms · the same entry in another collection · chain A against A, TM-score 1.00
- P08046 · AlphaFold monomer V2.0 prediction for early growth response protein 1 (P08046) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P08046
- Elsewhere: RCSB PDB 1ZAA · PDBe 1ZAA · UniProt P08046
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