Research workbench
PARVOVIRUS/DNA complex
Analyse PARVOVIRUS/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DPV
- Type
- protein + DNA
- Length
- 570 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (parvovirus coat protein); DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3')
- UniProt
- P17455
- Ligands
- MG
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z | Protein (parvovirus coat protein) | protein | 559 | 9% helix, 29% strand | P17455 |
| N | DNA (5'-D(*AP*TP*AP*CP*CP*TP*CP*TP*TP*GP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains Z, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.73 | 0.77 | 117 | empty |
| 2 | 110 | 0.63 | 0.88 | 23 | empty |
| 3 | 469 | 0.58 | 0.74 | 50 | empty |
| 4 | 92 | 0.48 | 0.81 | 23 | empty |
| 5 | 109 | 0.41 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- Z–N · 731 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4DPV · PARVOVIRUS/DNA complex · the same entry in another collection · chain Z against Z, 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 P17455
- Elsewhere: RCSB PDB 4DPV · PDBe 4DPV · UniProt P17455
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