4CP9

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
R-Value Work: 0.155
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05097
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 G [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D]	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 H [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D]	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 F [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D]	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 I [auth A] SDF format, chain W [auth D] MOL2 format, chain I [auth A] MOL2 format, chain W [auth D]	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 N [auth B] SDF format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [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 E [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D]	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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.184
R-Value Work: 0.155
R-Value Observed: 0.157
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

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

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4CP9

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2