MolNFT v1 · #92214 · protein + DNA
Structural characterization of H-1 parvovirus: comparison of infectious virions to replication defective particles
4G0R · Capsid protein VP1: “Structural characterization of H-1 parvovirus: comparison of infectious virions to replication defective…”. X-ray diffraction, 4 ligands (DC, NA, MG), 11 pockets (best druggability 0.73). MolNFT v1 #92214 on…
- PDB
- 4G0R
- Type
- protein + DNA
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; DNA (5'-D(P*CP*TP*GP*AP*CP*TP*TP*CP*AP*A)-3')
- UniProt
- P03136
- Ligands
- DC, NA, MG, CL
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 554 | 9% helix, 28% strand | P03136 |
| C | DNA (5'-D(P*CP*TP*GP*AP*CP*TP*TP*CP*AP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- DC · 2'-deoxycytidine-5'-monophosphate · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.73 | 0.99 | 17 | empty |
| 2 | 192 | 0.61 | 0.83 | 39 | empty |
| 3 | 386 | 0.57 | 0.74 | 44 | empty |
| 4 | 424 | 0.56 | 0.74 | 33 | empty |
| 5 | 153 | 0.49 | 0.78 | 36 | empty |
Interfaces
1 interface between chains.
- A–C · 691 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 4G0R · Structural characterization of H-1 Parvovirus: comparison of infectious virions to… · 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 P03136
- Elsewhere: RCSB PDB 4G0R · PDBe 4G0R · UniProt P03136
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