1JXN | pdb_00001jxn

Crystal Structure of the Lectin I from Ulex europaeus in complex with the methyl glycoside of alpha-L-fucose

PDB DOI: https://doi.org/10.2210/pdb1JXN/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ulex europaeus
Mutation(s): No

Deposited: 2001-09-07 Released: 2002-12-06
Deposition Author(s): Audette, G.F., Olson, D.J.H., Ross, A.R.S., Quail, J.W., Delbaere, L.T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.289 (Depositor)
R-Value Work:
0.202 (Depositor), 0.262 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Examination of the Structural Basis for O(H) Blood Group Specificity by Ulex europaeus Lectin I

Audette, G.F., Olson, D.J.H., Ross, A.R.S., Quail, J.W., Delbaere, L.T.J.

(2002) Can J Chem 80: 1010-1021

DOI: https://doi.org/10.1139/v02-134

Macromolecule Content

Total Structure Weight: 107.73 kDa
Atom Count: 7,773
Modeled Residue Count: 959
Deposited Residue Count: 968
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-H(O) lectin I	A, B, C, D	242	Ulex europaeus	Mutation(s): 0
UniProt
Find proteins for P22972 (Ulex europaeus) Explore P22972 Go to UniProtKB: P22972
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22972
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MFU Query on MFU Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], O [auth D]	methyl alpha-L-fucopyranoside C₇ H₁₄ O₅ OHWCAVRRXKJCRB-CXNFULCWSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C], P [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.289 (Depositor)
R-Value Work: 0.202 (Depositor), 0.262 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.81	α = 90
b = 69	β = 106.76
c = 119.02	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-12-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-12-06
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2024-10-30
Changes: Structure summary

1JXN | pdb_00001jxn

Crystal Structure of the Lectin I from Ulex europaeus in complex with the methyl glycoside of alpha-L-fucose

Literature

Examination of the Structural Basis for O(H) Blood Group Specificity by Ulex europaeus Lectin I

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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