MolNFT v1 · #152475 · protein + DNA
Complex structure of the HRP3 pwwp domain with both a 16-bp ta-rich DNA and an H3K36ME3-containing histone peptide
6IIS · Hepatoma-derived growth factor-related protein 3: “Complex structure of the HRP3 pwwp domain with both a 16-bp ta-rich DNA and an H3K36ME3-containing histone…”. X-ray diffraction, 2 pockets (best druggability 0.39). MolNFT v1…
- PDB
- 6IIS
- Type
- protein + DNA
- Length
- 228 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatoma-derived growth factor-related protein 3; 16-bp ta-rich DNA; H3K36ME3 peptide
- UniProt
- Q9Y3E1
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hepatoma-derived growth factor-related protein 3 | protein | 99 | 21% helix, 21% strand | Q9Y3E1 |
| C, D | 16-bp ta-rich DNA | dna | 10 | — | — |
| E, F | H3K36ME3 peptide | protein | 5 | 0% helix, 20% strand | — |
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 | 87 | 0.39 | 0.78 | 14 | empty |
| 2 | 62 | 0.27 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 435 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- B–F · 387 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 329 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 278 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 277 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6IIS · Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an… · 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 6IIS · PDBe 6IIS · UniProt Q9Y3E1
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