Research workbench
Crystal structure of the oligomerization domain of NSP4 from rotavirus strain MF66
Analyse Crystal structure of the oligomerization domain of NSP4 from rotavirus strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y9R
- Type
- protein
- Length
- 169 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nonstructural protein 4
- UniProt
- Q6QT01
- Ligands
- NI, CD
Structure
x-ray diffraction · 4 distinct chains · 94% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nonstructural protein 4 | protein | 45 | 93% helix, 0% strand | Q6QT01 |
| B | Nonstructural protein 4 | protein | 40 | 95% helix, 0% strand | Q6QT01 |
| D | Nonstructural protein 4 | protein | 44 | 95% helix, 0% strand | Q6QT01 |
| C | Nonstructural protein 4 | protein | 40 | 93% helix, 0% strand | Q6QT01 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B, D
- CD · Cadmium ion · metal · chains B, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- B–D · 842 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 742 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 691 Ų buried · 2 hydrogen bonds · protein-protein
- D–C · 657 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 495 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5Y9R · Crystal structure of the oligomerization domain of NSP4 from rotavirus strain MF66 · 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 Q6QT01
- Elsewhere: RCSB PDB 5Y9R · PDBe 5Y9R · UniProt Q6QT01
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