Research workbench
Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice
Analyse Structural determinants of tissue tropism and in vivo pathogenicity for the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z1C
- Type
- protein + DNA
- Length
- 570 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3'; 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3'; Coat…
- UniProt
- P07302
- Ligands
- D5M, CA
- Pockets
- 11 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3' | dna | 12 | — | — |
| C | 5'-D(*AP*CP*AP*CP*CP*AP*AP*AP*A)-3' | dna | 9 | — | — |
| A | Coat protein VP2 | protein | 549 | 8% helix, 26% strand | P07302 |
Ligands and binding sites
- D5M · 2'-deoxyadenosine-5'-monophosphate · ligand · chains B
- CA · Calcium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.60 | 0.75 | 41 | empty |
| 2 | 259 | 0.59 | 0.79 | 36 | empty |
| 3 | 173 | 0.55 | 0.80 | 29 | empty |
| 4 | 158 | 0.44 | 0.75 | 25 | empty |
| 5 | 157 | 0.42 | 0.73 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–C · 489 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- B–A · 208 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 1Z1C · Structural Determinants of Tissue Tropism and In Vivo Pathogenicity for the Parvovirus… · 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 P07302
- Elsewhere: RCSB PDB 1Z1C · PDBe 1Z1C · UniProt P07302
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.