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The crystal structure of macrobrachium rosenbergii nodavirus P-domain with CD ion
Analyse The crystal structure of macrobrachium rosenbergii nodavirus P-domain with CD… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YKX
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q6XNL3
- Ligands
- CD, SO4
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 118 | 0% helix, 57% strand | Q6XNL3 |
| B | Capsid protein | protein | 123 | 2% helix, 56% strand | Q6XNL3 |
Ligands and binding sites
- CD · Cadmium ion · metal · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 1377 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 5YKX · The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Cd ion · 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 Q6XNL3
- Elsewhere: RCSB PDB 5YKX · PDBe 5YKX · UniProt Q6XNL3
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