2PHU | pdb_00002phu

Pterocarpus angolensis lectin in complex with Man-8D1D3

PDB DOI: https://doi.org/10.2210/pdb2PHU/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pterocarpus angolensis
Mutation(s): No

Deposited: 2007-04-12 Released: 2007-07-10
Deposition Author(s): Garcia-Pino, A., Buts, L., Wyns, L., Imberty, A., Loris, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.209 (Depositor), 0.197 (DCC)
R-Value Work:
0.174 (Depositor), 0.163 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

How a plant lectin recognizes high mannose oligosaccharides

Garcia-Pino, A., Buts, L., Wyns, L., Imberty, A., Loris, R.

(2007) Plant Physiol 144: 1733-1741

PubMed: 17556509 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1104/pp.107.100867
Primary Citation Related Structures:
2PHF, 2PHR, 2PHT, 2PHU, 2PHW, 2PHX

PubMed Abstract:
The crystal structure of Pterocarpus angolensis seed lectin is presented in complex with a series of high mannose (Man) oligosaccharides ranging from Man-5 to Man-9. Despite that several of the nine Man residues of Man-9 have the potential to bind in the monosaccharide-binding site, all oligomannoses are bound in the same unique way, employing the tetrasaccharide sequence Manalpha(1-2)Manalpha(1-6)[Manalpha(1-3)]Manalpha(1-. Isothermal titration calorimetry titration experiments using Man-5, Man-9, and the Man-9-containing glycoprotein soybean (Glycine max) agglutinin as ligands confirm the monovalence of Man-9 and show a 4-times higher affinity for Man-9 when it is presented to P. angolensis seed lectin in a glycoprotein context.

Organizational Affiliation

Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium.

Macromolecule Content

Total Structure Weight: 56.5 kDa
Atom Count: 3,933
Modeled Residue Count: 482
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lectin	A, B	252	Pterocarpus angolensis	Mutation(s): 0
UniProt
Find proteins for Q8GSD2 (Pterocarpus angolensis) Explore Q8GSD2 Go to UniProtKB: Q8GSD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8GSD2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose	C	5		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G11308TN GlyCosmos: G11308TN GlyGen: G11308TN

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A, B	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.209 (Depositor), 0.197 (DCC)
R-Value Work: 0.174 (Depositor), 0.163 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.696	α = 90
b = 83.348	β = 90
c = 122.69	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-07-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-07-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Advisory, Refinement description
Version 2.0: 2019-12-25
Changes: Data collection, Database references, Derived calculations, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 3.2: 2024-10-16
Changes: Structure summary