4CP9 | pdb_00004cp9

Crystal structure OF lecA lectin complexed with a divalent galactoside at 1.65 angstrom

PDB DOI: https://doi.org/10.2210/pdb4CP9/pdb

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

Deposited: 2014-02-04 Released: 2014-10-08
Deposition Author(s): Topin, J., Varrot, A., Imberty, A., Wissinger, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.184 (Depositor), 0.193 (DCC)
R-Value Work:
0.155 (Depositor), 0.168 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Leca Ligand Identified from a Galactoside-Conjugate Array Inhibits Host Cell Invasion by Pseudomonas Aeruginosa.

Novoa, A., Eierhoff, T., Topin, J., Varrot, A., Barluenga, S., Imberty, A., Romer, W., Winssinger, N.

(2014) Angew Chem Int Ed Engl 53: 8885

PubMed: 25044671 Search on PubMed
DOI: https://doi.org/10.1002/anie.201402831
Primary Citation Related Structures:
4CP9, 4CPB

PubMed Abstract:
Lectin LecA is a virulence factor of Pseudomonas aeruginosa involved in lung injury, mortality, and cellular invasion. Ligands competing with human glycoconjugates for LecA binding are thus promising candidates to counteract P. aeruginosa infections. We have identified a novel divalent ligand from a focused galactoside(Gal)-conjugate array which binds to LecA with very high affinity (Kd = 82 nM). Crystal structures of LecA complexed with the ligand together with modeling studies confirmed its ability to chelate two binding sites of LecA. The ligand lowers cellular invasiveness of P. aeruginosa up to 90 % when applied in the range of 0.05-5 μM. Hence, this ligand might lead to the development of drugs against P. aeruginosa infection.

Organizational Affiliation

Department of Organic Chemistry, University of Geneva (Switzerland).

Macromolecule Content

Total Structure Weight: 55.39 kDa
Atom Count: 4,294
Modeled Residue Count: 484
Deposited Residue Count: 484
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I GALACTOPHILIC LECTIN	A	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05097
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I GALACTOPHILIC LECTIN	B, C, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05097
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CN8 Query on CN8 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], R [auth C], V [auth D]	(4S)-N-ethyl-4-{[N-methyl-3-(1-{2-[(4-sulfanylbenzoyl)amino]ethyl}-1H-1,2,3-triazol-4-yl)-L-alanyl]amino}-L-prolinamide C₂₂ H₃₂ N₈ O₃ S VTNMGGUGQYETGZ-SNRMKQJTSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain S [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain X [auth D] MOL2 format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain X [auth D] mmCIF format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B], S [auth C], X [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain X [auth D]
GAL Query on GAL Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B], Q [auth C], U [auth D]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain U [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain I [auth A] MOL2 format, chain W [auth D] MOL2 format, chain I [auth A] mmCIF format, chain W [auth D] mmCIF format, chain I [auth A]	I [auth A], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain W [auth D] Interactions & Density Focus chain I [auth A] Focus chain W [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	N [auth B], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], P [auth C], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain T [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on OCS	A	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS
TRO Query on TRO	A	L-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₃		TRP

Binding Affinity Annotations
ID	Source	Binding Affinity
GAL	BindingDB: 4CP9	Kd: 8.75e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.184 (Depositor), 0.193 (DCC)
R-Value Work: 0.155 (Depositor), 0.168 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.876	α = 90
b = 66.259	β = 90
c = 159.427	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-08
Type: Initial release
Version 1.1: 2015-04-22
Changes: Derived calculations, Non-polymer description, Other
Version 1.2: 2016-12-28
Changes: Structure summary
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary

4CP9 | pdb_00004cp9

Crystal structure OF lecA lectin complexed with a divalent galactoside at 1.65 angstrom

Literature

A Leca Ligand Identified from a Galactoside-Conjugate Array Inhibits Host Cell Invasion by Pseudomonas Aeruginosa.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2