1SFY | pdb_00001sfy

Crystal structure of recombinant Erythrina corallodandron Lectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.208 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

Effect of glycosylation on the structure of Erythrina corallodendron lectin.

Kulkarni, K.A.Srivastava, A.Mitra, N.Sharon, N.Surolia, A.Vijayan, M.Suguna, K.

(2004) Proteins 56: 821-827

  • DOI: https://doi.org/10.1002/prot.20168
  • Primary Citation Related Structures: 
    1SFY

  • PubMed Abstract: 

    The three-dimensional structure of the recombinant form of Erythrina corallodendron lectin, complexed with lactose, has been elucidated by X-ray crystallography at 2.55 A resolution. Comparison of this non-glycosylated structure with that of the native glycosylated lectin reveals that the tertiary and quaternary structures are identical in the two forms, with local changes observed at one of the glycosylation sites (Asn17). These changes take place in such a way that hydrogen bonds with the neighboring protein molecules in rECorL compensate those made by the glycan with the protein in ECorL. Contrary to an earlier report, this study demonstrates that the glycan attached to the lectin does not influence the oligomeric state of the lectin. Identical interactions between the lectin and the non-covalently bound lactose in the two forms indicate, in line with earlier reports, that glycosylation does not affect the carbohydrate specificity of the lectin. The present study, the first of its kind involving a glycosylated protein with a well-defined glycan and the corresponding deglycosylated form, provides insights into the structural aspects of protein glycosylation.


  • Organizational Affiliation
    • Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Macromolecule Content 

  • Total Structure Weight: 160.23 kDa 
  • Atom Count: 12,073 
  • Modeled Residue Count: 1,434 
  • Deposited Residue Count: 1,434 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lectin
A, B, C, D, E
A, B, C, D, E, F
239Erythrina corallodendronMutation(s): 0 
UniProt
Find proteins for P16404 (Erythrina corallodendron)
Explore P16404 
Go to UniProtKB:  P16404
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16404
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
G, H, I, J, K
G, H, I, J, K, L
2N/A
Glycosylation Resources
GlyTouCan: G84224TW
GlyCosmos: G84224TW
GlyGen: G84224TW

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN

Query on MN



Download:Ideal Coordinates CCD File
M [auth A]
O [auth B]
Q [auth C]
S [auth D]
U [auth E]
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
N [auth A]
P [auth B]
R [auth C]
T [auth D]
V [auth E]
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.208 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.24α = 90
b = 144.89β = 93.29
c = 127.66γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary