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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 v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: Macrobrachium rosenbergii nodavirus
Molecule: Capsid protein
UniProt: Q6XNL3
Ligands: CD, SO4

Structure

x-ray diffraction · resolution 2 · 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 Å² 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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