4AKD

High resolution structure of Mannose Binding lectin from Champedak (CMB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures and Binding Specificity of Galactose- and Mannose-Binding Lectins from Champedak: Differences from Jackfruit Lectins

Gabrielsen, M.Abdul-Rahman, P.S.Othman, S.Hashim, O.H.Cogdell, R.J.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 709

  • DOI: https://doi.org/10.1107/S2053230X14008966
  • Primary Citation of Related Structures:  
    4AK4, 4AKB, 4AKC, 4AKD

  • PubMed Abstract: 

    Galactose-binding and mannose-binding lectins from the champedak fruit, which is native to South-east Asia, exhibit useful potential clinical applications. The specificity of the two lectins for their respective ligands allows the detection of potential cancer biomarkers and monitoring of the glycosylated state of proteins in human serum and/or urine. To fully understand and expand the use of these natural proteins, their complete sequences and crystal structures are presented here, together with details of sugar binding.


  • Organizational Affiliation

    Institute of Molecular, Cell and Systems Biology, University of Glasgow, 120 University Avenue, Glasgow G12 8TA, Scotland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MANNOSE-SPECIFIC LECTIN KM+
A, B, C, D
150Artocarpus integerMutation(s): 0 
UniProt
Find proteins for Q7M1T4 (Artocarpus integer)
Explore Q7M1T4 
Go to UniProtKB:  Q7M1T4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7M1T4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
E [auth A]
F [auth B]
G [auth B]
H [auth B]
M [auth C]
E [auth A],
F [auth B],
G [auth B],
H [auth B],
M [auth C],
N [auth C],
R [auth C],
S [auth D]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth B]
J [auth B]
K [auth B]
L [auth B]
O [auth C]
I [auth B],
J [auth B],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
Q [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.887α = 90
b = 86.222β = 90
c = 95.373γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2014-06-18
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description