Research workbench
Cpv (strain D) mutant A300D, complex (viral COAT/DNA), VP2, PH=7.5, T=4 degrees C
Analyse Cpv (strain D) mutant A300D, complex (viral COAT/DNA), VP2, PH=7.5, T=4 degrees… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IJS
- Type
- protein + DNA
- Length
- 559 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3'); DNA (5'-D(*AP*C)-3'); Protein (parvovirus coat…
- UniProt
- P30129
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | DNA (5'-D(*CP*CP*AP*CP*CP*CP*CP*AP*A)-3') | dna | 9 | — | — |
| A | DNA (5'-D(*AP*C)-3') | dna | 2 | — | — |
| P | Protein (parvovirus coat protein) | protein | 548 | 4% helix, 27% strand | P30129 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.67 | 0.77 | 69 | empty |
| 2 | 398 | 0.55 | 0.74 | 37 | empty |
| 3 | 287 | 0.54 | 0.76 | 38 | empty |
| 4 | 77 | 0.43 | 0.81 | 26 | empty |
| 5 | 115 | 0.41 | 0.76 | 24 | empty |
Interfaces
2 interfaces between chains.
- N–P · 213 Ų buried · 5 hydrogen bonds · protein-nucleic
- N–A · 146 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1IJS · CPV (STRAIN D) mutant A300D, complex (VIRAL COAT/DNA), VP2, PH=7.5, T=4 DEGREES C · the same entry in another collection · chain N against N, 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 P30129
- Elsewhere: RCSB PDB 1IJS · PDBe 1IJS · UniProt P30129
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