1XXR | pdb_00001xxr

Structure of a mannose-specific jacalin-related lectin from Morus Nigra in complex with mannose

PDB DOI: https://doi.org/10.2210/pdb1XXR/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Morus nigra
Mutation(s): No

Deposited: 2004-11-08 Released: 2005-10-25
Deposition Author(s): Rabijns, A., Barre, A., Van Damme, E.J.M., Peumans, W.J., De Ranter, C.J., Rouge, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.211 (Depositor), 0.200 (DCC)
R-Value Work:
0.191 (Depositor), 0.180 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural analysis of the jacalin-related lectin MornigaM from the black mulberry (Morus nigra) in complex with mannose

Rabijns, A., Barre, A., Van Damme, E.J.M., Peumans, W.J., De Ranter, C.J., Rouge, P.

(2005) FEBS J 272: 3725-3732

PubMed: 16008570 Search on PubMed
DOI: https://doi.org/10.1111/j.1742-4658.2005.04801.x
Primary Citation of Related Structures:
1XXQ, 1XXR

PubMed Abstract:
The structures of MornigaM and the MornigaM-mannose complex have been determined at 1.8 A and 2.0 A resolution, respectively. Both structures adopt the typical beta-prism motif found in other jacalin-related lectins and their tetrameric assembly closely resembles that of jacalin. The carbohydrate-binding cavity of MornigaM readily binds mannose. No major structural rearrangements can be observed in MornigaM upon binding of mannose. These results allow corroboration of the structure-function relationships within the small group of Moraceae lectins.

Organizational Affiliation

Laboratory of Analytical Chemistry and Medicinal Physicochemistry, Faculty of Pharmaceutical Sciences, K. U. Leuven, Belgium.

Macromolecule Content

Total Structure Weight: 69.05 kDa
Atom Count: 5,223
Modelled Residue Count: 616
Deposited Residue Count: 644
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mannose-binding lectin	A, B, C, D	161	Morus nigra	Mutation(s): 0
UniProt
Find proteins for Q8LGR3 (Morus nigra) Explore Q8LGR3 Go to UniProtKB: Q8LGR3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8LGR3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	G [auth B], I [auth C], K [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], J [auth C], L [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.211 (Depositor), 0.200 (DCC)
R-Value Work: 0.191 (Depositor), 0.180 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.908	α = 90
b = 110.908	β = 90
c = 160.021	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-10-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-10-25
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2024-03-13
Changes: Data collection, Database references, Structure summary