Research workbench
Crystal structure of N-terminal replicase protein of porcine circovirus type 2
Analyse Crystal structure of N-terminal replicase protein of porcine circovirus type 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XOR
- Type
- protein
- Length
- 492 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rep protein
- UniProt
- A9YPG7
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rep protein | protein | 98 | 28% helix, 42% strand | A9YPG7 |
| B | Rep protein | protein | 101 | 28% helix, 41% strand | A9YPG7 |
| C | Rep protein | protein | 99 | 27% helix, 40% strand | A9YPG7 |
| D | Rep protein | protein | 98 | 29% helix, 41% strand | A9YPG7 |
| E | Rep protein | protein | 96 | 27% helix, 43% strand | A9YPG7 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.47 | 0.77 | 24 | empty |
| 2 | 58 | 0.34 | 0.78 | 14 | empty |
| 3 | 77 | 0.34 | 0.75 | 20 | empty |
| 4 | 59 | 0.32 | 0.76 | 13 | empty |
| 5 | 55 | 0.30 | 0.76 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–E · 508 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 505 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 408 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 87 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5XOR · Crystal structure of N-terminal replicase protein of porcine circovirus type 2 · 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 A9YPG7
- Elsewhere: RCSB PDB 5XOR · PDBe 5XOR · UniProt A9YPG7
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