Research workbench
MOUSEZFP568-ZNF1-11 in complex with DNA
Analyse MOUSEZFP568-ZNF1-11 in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V3M
- Type
- protein + DNA
- Length
- 333 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (28-mer); Zinc finger protein 568
- UniProt
- E9PYI1
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (28-mer) | dna | 28 | — | — |
| B | DNA (28-mer) | dna | 28 | — | — |
| C | Zinc finger protein 568 | protein | 277 | 38% helix, 13% strand | E9PYI1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.74 | 0.79 | 64 | empty |
| 2 | 271 | 0.66 | 0.83 | 34 | empty |
| 3 | 205 | 0.61 | 0.83 | 25 | empty |
| 4 | 66 | 0.60 | 0.91 | 14 | empty |
| 5 | 78 | 0.51 | 0.85 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1888 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–B · 1302 Ų buried · 126 hydrogen bonds · nucleic-nucleic
- B–C · 1246 Ų buried · 14 hydrogen bonds · protein-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 E9PYI1
- Elsewhere: RCSB PDB 5V3M · PDBe 5V3M · UniProt E9PYI1
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