MolNFT v1 · #29206 · protein + DNA
Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice
1Z1C · 5'-D(*AP*TP*CP*CP*TP*CP*TP*AP*TP*CP*AP*C)-3': “Structural determinants of tissue tropism and in vivo pathogenicity for the parvovirus minute virus of mice”. X-ray diffraction, 2 ligands (D5M, CA), 11 pockets (best druggability…
- 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
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