Research workbench
Crystal structure of the nipah virus RNA free nucleoprotein-phosphoprotein complex
Analyse Crystal structure of the nipah virus RNA free nucleoprotein-phosphoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CO6
- Type
- protein
- Length
- 970 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; Phosphoprotein
- UniProt
- Q9IK92, Q9IK91
- Ligands
- CL, BR
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 330 | 66% helix, 6% strand | Q9IK92 |
| B | Nucleoprotein | protein | 324 | 66% helix, 6% strand | Q9IK92 |
| C | Nucleoprotein | protein | 200 | 79% helix, 0% strand | Q9IK92 |
| D | Phosphoprotein | protein | 40 | 73% helix, 0% strand | Q9IK91 |
| E | Phosphoprotein | protein | 39 | 72% helix, 0% strand | Q9IK91 |
| F | Phosphoprotein | protein | 37 | 73% helix, 0% strand | Q9IK91 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.71 | 0.80 | 45 | CL |
| 2 | 430 | 0.69 | 0.81 | 48 | empty |
| 3 | 445 | 0.69 | 0.80 | 62 | empty |
| 4 | 309 | 0.54 | 0.75 | 38 | BR |
| 5 | 53 | 0.44 | 0.84 | 17 | CL |
Interfaces
7 interfaces between chains.
- C–E · 1365 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 1333 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1295 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 601 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 454 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 4CO6 · Crystal structure of the Nipah virus RNA free nucleoprotein- phosphoprotein complex · 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 Q9IK92
- Every structure of UniProt Q9IK91
- Elsewhere: RCSB PDB 4CO6 · PDBe 4CO6 · UniProt Q9IK92 · UniProt Q9IK91
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