1ABR

CRYSTAL STRUCTURE OF ABRIN-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of abrin-a at 2.14 A.

Tahirov, T.H.Lu, T.H.Liaw, Y.C.Chen, Y.L.Lin, J.Y.

(1995) J.Mol.Biol. 250: 354-367

  • DOI: 10.1006/jmbi.1995.0382
  • Also Cited By: 2ZR1

  • PubMed Abstract: 
  • The crystal structure of abrin-a, a type II ribosome-inactivating protein from the seeds of Abrus precatorius, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of ricin. The structure has bee ...

    The crystal structure of abrin-a, a type II ribosome-inactivating protein from the seeds of Abrus precatorius, has been determined from a novel crystalline form by the molecular replacement method using the coordinates of ricin. The structure has been refined at 2.14 A to a R-factor of 18.9%. The root-mean-square deviations of bond lengths and angles from the standard values are 0.013 A and 1.82 degrees, respectively. The overall protein folding is similar to that of ricin, but there are differences in the secondary structure, mostly of the A-chain. Several parts of the molecular surface differ significantly; some of them are quite near the active site cleft, and probably influence ribosome recognition. The positions of invariant active site residues remain the same, except the position of Tyr74. Two water molecules of hydrogen-bonded active site residues have been located in the active site cleft. Both of them may be responsible for hydrolyzing the N-C glycosidic bond. The current abrin-a structure is lactose free; this is probably essential for abrin-a crystallization. The B-chain is a glycoprotein, and the positions of several sugar residues of two sugar chains linked to earlier predicted glycosylation sites were determined. One of the sugar chains is a bridge between two neighboring molecules, since one of its mannose residues is connected to the galactose binding site of the neighboring molecule. Another sugar chain covers the surface of the B-chain.


    Related Citations: 
    • Primary Structure of Three Distinct Isobrins Determined by Cdna Sequencing: Conservation and Significance
      Hung, C.-H.,Lee, M.-C.,Lee, T.-C.,Lin, J.-Y.
      (1993) J.Mol.Biol. 229: 263
    • The Complete Amino Acid Sequence of the A-Chain of Abrin-1, a Toxic Protein from the Seeds of Abrus Precatorius
      Fanatsu, G.,Taguchi, Y.,Kamenosono, M.,Yanaka, M.
      (1988) J.Biol.Chem. 52: 1095
    • A New Crystal Form of Abrin-A from the Seeds of Abrus Precatorius
      Tahirov, T.H.,Lu, T.-H.,Liaw, Y.-C.,Chu, S.-C.,Lin, J.-Y.
      (1994) J.Mol.Biol. 235: 1152


    Organizational Affiliation

    Department of Physics, National Tsing Hua University, Hsinchu, Taiwan, Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABRIN-A
A
251Abrus precatoriusMutation(s): 0 
Find proteins for P11140 (Abrus precatorius)
Go to UniProtKB:  P11140
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ABRIN-A
B
267Abrus precatoriusMutation(s): 0 
Find proteins for P11140 (Abrus precatorius)
Go to UniProtKB:  P11140
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGZ
Query on NGZ

Download SDF File 
Download CCD File 
B
2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-DMHSOCPYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
B
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.580α = 90.00
b = 73.070β = 96.20
c = 48.230γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-07
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance