MolNFT v1 · #138458 · protein + DNA
MOUSEZFP568-ZNF2-11 in complex with DNA
5WJQ · DNA (28-mer): “MOUSEZFP568-ZNF2-11 in complex with DNA”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.71). MolNFT v1 #138458 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WJQ
- Type
- protein + DNA
- Length
- 337 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
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (28-mer) | dna | 28 | — | — |
| B | DNA (28-mer) | dna | 28 | — | — |
| D | Zinc finger protein 568 | protein | 281 | 38% helix, 12% strand | E9PYI1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.71 | 0.80 | 40 | empty |
| 2 | 243 | 0.63 | 0.82 | 32 | empty |
| 3 | 59 | 0.63 | 0.93 | 15 | empty |
| 4 | 87 | 0.51 | 0.84 | 15 | empty |
| 5 | 99 | 0.49 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–D · 2280 Ų buried · 49 hydrogen bonds · protein-nucleic
- B–D · 1302 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 1266 Ų buried · 109 hydrogen bonds · nucleic-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 5WJQ · PDBe 5WJQ · UniProt E9PYI1
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