MolNFT v1 · #152474 · protein + DNA
Complex structure of the HRP3 pwwp domain with a 10-bp gc-rich DNA
6IIR · Hepatoma-derived growth factor-related protein 3: “Complex structure of the HRP3 pwwp domain with a 10-bp gc-rich DNA”. X-ray diffraction, 2 pockets (best druggability 0.52). MolNFT v1 #152474 on GenesisL1: 3D structure, binding…
- PDB
- 6IIR
- Type
- protein + DNA
- Length
- 217 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatoma-derived growth factor-related protein 3; 10-bp gc-rich DNA
- UniProt
- Q9Y3E1
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatoma-derived growth factor-related protein 3 | protein | 98 | 21% helix, 21% strand | Q9Y3E1 |
| B | Hepatoma-derived growth factor-related protein 3 | protein | 99 | 21% helix, 21% strand | Q9Y3E1 |
| C, D | 10-bp gc-rich DNA | dna | 10 | — | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.52 | 0.81 | 18 | empty |
| 2 | 58 | 0.39 | 0.80 | 12 | empty |
Interfaces
4 interfaces between chains.
- C–D · 496 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–D · 179 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–C · 178 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–C · 150 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 6IIR · Complex structure of the HRP3 PWWP domain with a 10-bp GC-rich DNA · the same entry in another collection · chain C against C, TM-score 1.00
- Q9Y3E1 · AlphaFold monomer V2.0 prediction for hepatoma-derived growth factor- related protein 3… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9Y3E1
- Elsewhere: RCSB PDB 6IIR · PDBe 6IIR · UniProt Q9Y3E1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.