4XTP

Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with Tn antigen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of a recombinant Vatairea macrocarpa seed lectin

Sousa, B.L.Silva-Filho, J.C.Kumar, P.Lyskowski, A.Bezerra, G.A.Delatorre, P.Rocha, B.A.M.Cunha, R.M.S.Nagano, C.S.Gruber, K.Cavada, B.S.

(2016) Int.J.Biochem.Cell Biol. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Seed lectin
A
250Vatairea macrocarpaMutation(s): 0 
Find proteins for P81371 (Vatairea macrocarpa)
Go to UniProtKB:  P81371
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
TNR
Query on TNR

Download SDF File 
Download CCD File 
A
O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)-L-SERINE
C11 H20 N2 O8
REDMNGDGDYFZRE-WKWISIMFSA-N
 Ligand Interaction
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 56.093α = 90.00
b = 86.024β = 90.00
c = 128.877γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction
PHASERphasing
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release