MolNFT v1 · #126925 · protein + DNA
ICP4 DNA-binding domain in complex with 19MER DNA duplex from its own promoter
5MHK · DNA (5'- D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*…: “ICP4 DNA-binding domain in complex with 19MER DNA duplex from its own promoter”. X-ray diffraction, 3 ligands (MG, SO4, CL), 10 pockets (best druggability 0.81). MolNFT…
- PDB
- 5MHK
- Type
- protein + DNA
- Length
- 845 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3'); RS1; ICP4 DNA…
- UniProt
- Q09I77
- Ligands
- MG, SO4, CL
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 51% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA (5'- D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3') | dna | 19 | — | — |
| H | DNA (5'- D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3') | dna | 18 | — | — |
| E | DNA (5'- D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3') | dna | 15 | — | — |
| F | DNA (5'- D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3') | dna | 16 | — | — |
| A | RS1 | protein | 186 | 52% helix, 4% strand | Q09I77 |
| C | RS1 | protein | 195 | 52% helix, 3% strand | Q09I77 |
| D | RS1 | protein | 197 | 51% helix, 4% strand | Q09I77 |
| B | RS1 | protein | 197 | 52% helix, 3% strand | Q09I77 |
| J | ICP4 DNA binding domain | protein | 2 | 0% helix, 0% strand | Q09I77 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains H, A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, F, C, H, D, B
- CL · Chloride ion · ion · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.81 | 0.82 | 98 | SO4 |
| 2 | 897 | 0.80 | 0.83 | 93 | SO4 |
| 3 | 827 | 0.79 | 0.83 | 92 | SO4 |
| 4 | 1057 | 0.78 | 0.80 | 82 | SO4 |
| 5 | 254 | 0.62 | 0.81 | 33 | empty |
Interfaces
20 interfaces between chains.
- C–D · 3319 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3195 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 848 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- E–F · 708 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- G–C · 476 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5MHK · ICP4 DNA-binding domain in complex with 19mer DNA duplex from its own promoter · the same entry in another collection · chain G against G, 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
- Every structure of UniProt Q09I77
- Elsewhere: RCSB PDB 5MHK · PDBe 5MHK · UniProt Q09I77
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.