MolNFT v1 · #17789 · protein + DNA
Crystal structure of tandem ZIF268 molecules complexed to DNA
1P47 · 5'- D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP…: “Crystal structure of tandem ZIF268 molecules complexed to DNA”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.65). MolNFT v1 #17789 on GenesisL1: 3D…
- PDB
- 1P47
- Type
- protein + DNA
- Length
- 215 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP*GP *CP*GP*T)-3'; 5'…
- UniProt
- P08046
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- D(*GP*TP*GP*GP*CP*GP*TP*GP*GP*GP*CP*GP*GP*CP*GP*TP*GP*GP*GP *CP*GP*T)-3' | dna | 22 | — | — |
| D | 5'- D(*CP*AP*CP*GP*CP*CP*CP*AP*CP*GP*CP*CP*GP*CP*CP*CP*AP*CP*GP *CP*CP*A)-3' | dna | 22 | — | — |
| A | Early growth response protein 1 | protein | 87 | 37% helix, 14% strand | P08046 |
| B | Early growth response protein 1 | protein | 84 | 38% helix, 12% strand | P08046 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
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 | 140 | 0.65 | 0.87 | 16 | empty |
| 2 | 72 | 0.63 | 0.92 | 17 | empty |
| 3 | 88 | 0.62 | 0.90 | 16 | empty |
| 4 | 74 | 0.60 | 0.90 | 17 | empty |
| 5 | 81 | 0.54 | 0.86 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–A · 1118 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–B · 1082 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–D · 1012 Ų buried · 110 hydrogen bonds · nucleic-nucleic
- D–A · 570 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–B · 541 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 1P47 · Crystal Structure of tandem Zif268 molecules complexed to DNA · the same entry in another collection · chain C against C, 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 B 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 1P47 · PDBe 1P47 · UniProt P08046
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.