Research workbench
Structure of nuclease domain of human parvovirus B19 non-structural protein 1 in complex with zinc
Analyse Structure of nuclease domain of human parvovirus B19 non-structural protein 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6USM
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin-binding protein; Non-structural protein NS1
- UniProt
- C3SHQ8, Q6TV13
- Ligands
- GLC, ZN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltodextrin-binding protein | protein | 368 | 45% helix, 20% strand | C3SHQ8 |
| B | Non-structural protein NS1 | protein | 164 | 35% helix, 16% strand | Q6TV13 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.70 | 0.88 | 31 | empty |
| 2 | 312 | 0.70 | 0.83 | 36 | GLC |
| 3 | 515 | 0.66 | 0.77 | 70 | empty |
| 4 | 73 | 0.41 | 0.79 | 16 | empty |
| 5 | 62 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 874 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6USM · Structure of nuclease domain of human parvovirus B19 non-structural protein 1 in complex… · the same entry in another collection · chain A against A, 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 C3SHQ8
- Every structure of UniProt Q6TV13
- Elsewhere: RCSB PDB 6USM · PDBe 6USM · UniProt C3SHQ8 · UniProt Q6TV13
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