MolNFT v1 · #140407 · protein
Crystal structure of the oligomerization domain of NSP4 from rotavirus strain MF66
5Y9R · Nonstructural protein 4: “Crystal structure of the oligomerization domain of NSP4 from rotavirus strain MF66”. X-ray diffraction, 2 ligands (NI, CD). MolNFT v1 #140407 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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