Research workbench
Crystal structure of a designed zinc finger protein bound to DNA
Analyse Crystal structure of a designed zinc finger protein bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MEY
- Type
- protein + DNA
- Length
- 247 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3'); DNA (5'…
- Ligands
- ZN, CL
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA (5'- D(*AP*TP*GP*AP*GP*GP*CP*AP*GP*AP*AP*CP*T)-3') | dna | 13 | — | — |
| B, E | DNA (5'- D(*TP*AP*GP*TP*TP*CP*TP*GP*CP*CP*TP*(C38)P*A)-3') | dna | 13 | — | — |
| C | Consensus zinc finger | protein | 83 | 41% helix, 14% strand | — |
| F | Consensus zinc finger | protein | 84 | 42% helix, 14% strand | — |
| G | Consensus zinc finger | protein | 28 | 29% helix, 14% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.45 | 0.81 | 15 | empty |
| 2 | 157 | 0.43 | 0.75 | 30 | ZN, CL |
| 3 | 54 | 0.37 | 0.80 | 15 | empty |
| 4 | 65 | 0.33 | 0.76 | 16 | empty |
Interfaces
12 interfaces between chains.
- D–F · 963 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–C · 923 Ų buried · 23 hydrogen bonds · protein-nucleic
- D–E · 549 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- A–B · 540 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- E–F · 538 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1MEY · Crystal structure of a designed zinc finger protein bound to DNA · the same entry in another collection · chain C against C, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1MEY · PDBe 1MEY
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