4AL9

Crystal structure of the lectin PA-IL from Pseudomonas aeruginoas in complex with melibiose

PDB DOI: https://doi.org/10.2210/pdb4AL9/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-02 Released: 2013-03-20
Deposition Author(s): Blanchard, B., Imberty, A., Varrot, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.211
R-Value Work: 0.167
R-Value Observed: 0.169

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Secondary Sugar Binding Site Identified for Leca Lectin from Pseudomonas Aeruginosa.

Blanchard, B., Imberty, A., Varrot, A.

(2014) Proteins 82: 1060

PubMed: 24123124 Search on PubMed
DOI: https://doi.org/10.1002/prot.24430
Primary Citation of Related Structures:
4AL9

PubMed Abstract:
The galactose-specific lectin LecA from Pseudomonas aeruginosa is a target for the development of new anti-infectious compounds. Sugar based molecules with anti-adhesive properties present great potential in the fight against bacterial infection and biofilm formation. LecA is specific for oligosaccharides with terminal α-galactoside residues and displays strong affinity for melibiose (αGal1-6Glc) with a Kd of 38.8 µM. The crystal structure of LecA/melibiose complex shows classical calcium-bridged binding of αGal in the primary binding site but also revealed a secondary sugar binding site with glucose bound. This sugar binding site is in close proximity to the galactose binding one, is independent of calcium and mainly involves interactions with a symmetry-related protein. This discovery would help to the design of new potent inhibitors targeting both binding sites.

Organizational Affiliation

CERMAV-CNRS, Université de Grenoble and Member of ICMG, BP 53, 38041 Grenoble Cedex 9, France.

Macromolecule Content

Total Structure Weight: 104.56 kDa
Atom Count: 8,195
Modelled Residue Count: 968
Deposited Residue Count: 968
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I GALACTOPHILIC LECTIN	A, B, C, D, E A, B, C, D, E, F, G, H	121	Pseudomonas aeruginosa PAO1	Mutation(s): 0
UniProt
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q05097 Go to UniProtKB: Q05097
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05097
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose	I, J	2		N/A	Interactions Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G54976AD GlyCosmos: G54976AD GlyGen: G54976AD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLA Query on GLA Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain V [auth E] MOL2 format, chain AA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] mmCIF format, chain AA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E]	AA [auth G] L [auth A] O [auth B] Q [auth C] S [auth D] AA [auth G], L [auth A], O [auth B], Q [auth C], S [auth D], V [auth E]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain AA [auth G] Focus chain L [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain V [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain M [auth A] SDF format, chain T [auth D] SDF format, chain W [auth F] SDF format, chain Y [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain T [auth D] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain T [auth D] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth F]	BA [auth H], M [auth A], T [auth D], W [auth F], Y [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain M [auth A] Focus chain T [auth D] Focus chain W [auth F] Focus chain Y [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain X [auth F] SDF format, chain Z [auth G] SDF format, chain CA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain CA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain CA [auth H]	CA [auth H] K [auth A] N [auth B] P [auth C] R [auth D] CA [auth H], K [auth A], N [auth B], P [auth C], R [auth D], U [auth E], X [auth F], Z [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Focus chain K [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Binding Affinity Annotations
ID	Source	Binding Affinity
GLA	BindingDB: 4AL9	Kd: min: 8.75e+4, max: 8.80e+4 (nM) from 2 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900037 Query on PRD_900037	I, J	alpha-melibiose	Oligosaccharide / Metabolism		Interactions Focus chain I Focus chain J

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.211
R-Value Work: 0.167
R-Value Observed: 0.169
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.07	α = 101.13
b = 58.13	β = 92.89
c = 75.94	γ = 100.98

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

Blanchard, B.

Imberty, A.

Varrot, A.

Revision History (Full details and data files)

Version 1.0: 2013-03-20
Type: Initial release
Version 1.1: 2013-10-30
Changes: Database references
Version 1.2: 2014-05-28
Changes: Database references
Version 1.3: 2015-09-16
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary