MolNFT v1 · #139862 · protein + DNA
Crystal structure of pwwp-DNA complex for human hepatoma-derived growth factor
5XSK · DNA (5'-D(P*TP*TP*CP*AP*AP*GP*AP*CP*CP*A)-3'): “Crystal structure of pwwp-DNA complex for human hepatoma-derived growth factor”. X-ray diffraction, 2 pockets (best druggability 0.48). MolNFT v1 #139862 on GenesisL1: 3D structure…
- PDB
- 5XSK
- Type
- protein + DNA
- Length
- 201 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*TP*TP*CP*AP*AP*GP*AP*CP*CP*A)-3'); DNA…
- UniProt
- Q8VHK7
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'-D(P*TP*TP*CP*AP*AP*GP*AP*CP*CP*A)-3') | dna | 10 | — | — |
| F | DNA (5'-D(P*TP*GP*GP*TP*CP*TP*TP*GP*AP*A)-3') | dna | 10 | — | — |
| A | Hepatoma-derived growth factor | protein | 90 | 24% helix, 24% strand | Q8VHK7 |
| B | Hepatoma-derived growth factor | protein | 91 | 22% helix, 24% strand | Q8VHK7 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.48 | 0.78 | 22 | empty |
| 2 | 123 | 0.38 | 0.73 | 30 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2771 Ų buried · 42 hydrogen bonds · protein-protein
- D–F · 432 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- F–A · 184 Ų buried · 3 hydrogen bonds · protein-nucleic
- D–B · 149 Ų buried · 2 hydrogen bonds · protein-nucleic
- D–A · 62 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5XSK · Crystal structure of PWWP-DNA complex for human hepatoma-derived growth factor · the same entry in another collection · chain D against D, TM-score 1.00
- Q8VHK7 · AlphaFold monomer V2.0 prediction for hepatoma-derived growth factor (Q8VHK7) · a predicted model of the same protein · chain A against A, TM-score 0.62
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 Q8VHK7
- Elsewhere: RCSB PDB 5XSK · PDBe 5XSK · UniProt Q8VHK7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.