3PA1

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with HBGA type A

Structural Biology Knowledgebase: 3PA1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.178

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3PA1

Classification: VIRAL PROTEIN

Total Structure Weight: 71209.29

Macromolecule Entities
Molecule Chains Length Organism Details
Capsid protein A, B 319 Norwalk virus Fragment: P-domain-026 (UNP residues 224 to 538)
Gene Name(s):

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
A2G
Query on A2G

A N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

A BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A, B IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.178
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.19 α = 90.00
b = 78.99 β = 101.06
c = 70.10 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-10-18
  • Released Date: 2011-05-11
  • Deposition author(s): Hansman, G.S., Biertumpfel, C., Chen, L., Georgiev, I., McLellan, J.S., Katayama, K., Kwong, P.D.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4