1KQR

Crystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain in Complex with 2-O-methyl-alpha-D-N-acetyl neuraminic acid

Structural Biology Knowledgebase: 1KQR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1KQR

Classification: Viral protein

Total Structure Weight: 20731.95

Macromolecule Entities
Molecule Chains Length Organism Details
VP4 A 179 Rotavirus a Fragment: sialic acid binding domain (residues 62-224)
Gene Name(s):

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MNA
Query on MNA

A 2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
C12 H21 N O9
NJRVVFURCKKXOD-MIDKXNQYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.169
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.03 α = 90.00
b = 48.03 β = 90.00
c = 130.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-07
  • Released Date: 2002-03-27
  • Deposition author(s): Dormitzer, P.R., Sun, Z.-Y.J., Wagner, G., Harrison, S.C.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4