5J50 | pdb_00005j50

Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.187 (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

Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP

Abhinav, K.V., Sharma, K., Surolia, A., Vijayan, M.

To be published.

Macromolecule Content 

  • Total Structure Weight: 69.41 kDa 
  • Atom Count: 5,143 
  • Modeled Residue Count: 594 
  • Deposited Residue Count: 608 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Agglutinin alpha chain
A, C, E, G
133Artocarpus integerMutation(s): 0 
UniProt
Find proteins for P18670 (Artocarpus integer)
Explore P18670 
Go to UniProtKB:  P18670
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18670
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Agglutinin beta-3 chain
B, D, F, H
19Artocarpus integerMutation(s): 0 
UniProt
Find proteins for P18673 (Artocarpus integer)
Explore P18673 
Go to UniProtKB:  P18673
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18673
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose
I, J, K, L
2N/A
Glycosylation Resources
GlyTouCan: G00031MO
GlyCosmos: G00031MO
GlyGen: G00031MO

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NPO

Query on NPO


Download:Ideal Coordinates CCD File
BA [auth G],
P [auth A],
Q [auth C],
Y [auth E]		P-NITROPHENOL
C6 H5 N O3
BTJIUGUIPKRLHP-UHFFFAOYSA-N
PEG

Query on PEG


Download:Ideal Coordinates CCD File
V [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth G]
CA [auth H]
M [auth A]
N [auth A]
O [auth A]
AA [auth G],
CA [auth H],
M [auth A],
N [auth A],
O [auth A],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
W [auth E],
X [auth E],
Z [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.53α = 90
b = 81.65β = 100
c = 66.89γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Science and Technology, Govt. of IndiaIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary