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 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Seed lectinA250Vatairea macrocarpaMutation(s): 0 
UniProt
Find proteins for P81371 (Vatairea macrocarpa)
Explore P81371 
Go to UniProtKB:  P81371
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81371
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A2G
Query on A2G

Download Ideal Coordinates CCD File 
M [auth A]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
D [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SER
Query on SER

Download Ideal Coordinates CCD File 
L [auth A]SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth 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 
  • R-Value Observed: 0.201 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.093α = 90
b = 86.024β = 90
c = 128.877γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary