Research workbench
PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in complex with Z57475068
Analyse PanDDA analysis group deposition -- Crystal structure of HRP-2 PWWP domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7HGI
- Type
- protein
- Length
- 265 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.71
- Source
- Homo sapiens
- Molecule
- Hepatoma-derived growth factor-related protein 2
- UniProt
- Q7Z4V5
- Ligands
- A1A35, SO4
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · resolution 1.71 · 3 distinct chains · 24% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hepatoma-derived growth factor-related protein 2 | protein | 93 | 23% helix, 24% strand | Q7Z4V5 |
| B | Hepatoma-derived growth factor-related protein 2 | protein | 89 | 24% helix, 25% strand | Q7Z4V5 |
| C | Hepatoma-derived growth factor-related protein 2 | protein | 83 | 25% helix, 25% strand | Q7Z4V5 |
Ligands and binding sites
- A1A35 · N~1~,N~1~,N~4~,N~4~-tetramethylpiperazine-1,4-dicarboxamide · ligand · 2 copies · chains B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.40 | 0.81 | 12 | A1A35 |
Interfaces
2 interfaces between chains.
- A–C · 430 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 355 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- Q7Z4V5 · AlphaFold monomer V2.0 prediction for hepatoma-derived growth factor- related protein 2… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q7Z4V5
- Elsewhere: RCSB PDB 7HGI · PDBe 7HGI · UniProt Q7Z4V5
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