2CCV | pdb_00002ccv

Structure of Helix Pomatia agglutinin with zinc and N-acetyl-alpha-D- galactoseamine (GalNAc)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.179 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.157 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Biochemical and Structural Analysis of Helix Pomatia Agglutinin. A Hexameric Lectin with a Novel Fold.

Sanchez, J.-F.Lescar, J.Chazalet, V.Audfray, A.Gagnon, J.Alvarez, R.Breton, C.Imberty, A.Mitchell, E.P.

(2006) J Biological Chem 281: 20171

  • DOI: https://doi.org/10.1074/jbc.M603452200
  • Primary Citation Related Structures: 
    2CCV, 2CE6

  • PubMed Abstract: 

    Helix pomatia agglutinin (HPA) is a N-acetylgalactosamine (GalNAc) binding lectin found in the albumen gland of the roman snail. As a constituent of perivitelline fluid, HPA protects fertilized eggs from bacteria and is part of the innate immunity system of the snail. The peptide sequence deduced from gene cloning demonstrates that HPA belongs to a family of carbohydrate-binding proteins recently identified in several invertebrates. This domain is also present in discoidin from the slime mold Dictyostelium discoideum. Investigation of the lectin specificity was performed with the use of glycan arrays, demonstrating that several GalNAc-containing oligosaccharides are bound and rationalizing the use of this lectin as a cancer marker. Titration microcalorimetry performed on the interaction between HPA and GalNAc indicates an affinity in the 10(-4) M range with an enthalpy-driven binding mechanism. The crystal structure of HPA demonstrates the occurrence of a new beta-sandwich lectin fold. The hexameric quaternary state was never observed previously for a lectin. The high resolution structure complex of HPA with GalNAc characterizes a new carbohydrate binding site and rationalizes the observed preference for alphaGalNAc-containing oligosaccharides.


  • Organizational Affiliation
    • Centre de Recherches sur les Macromolécules Végétales, CNRS, Université Joseph Fourier, 38041 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 11.99 kDa 
  • Atom Count: 962 
  • Modeled Residue Count: 99 
  • Deposited Residue Count: 101 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HELIX POMATIA AGGLUTININ101Helix pomatiaMutation(s): 0 
UniProt
Find proteins for Q2F1K8 (Helix pomatia)
Explore Q2F1K8 
Go to UniProtKB:  Q2F1K8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2F1K8
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
A2G

Query on A2G



Download:Ideal Coordinates CCD File
C [auth A]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.179 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.157 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.45α = 90
b = 48.45β = 90
c = 286.12γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
HYSSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary