1OKO | pdb_00001oko

Crystal structure of Pseudomonas Aeruginosa Lectin 1 complexed with galactose at 1.6 A resolution

PDB DOI: https://doi.org/10.2210/pdb1OKO/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa
Mutation(s): No

Deposited: 2003-07-28 Released: 2003-12-04
Deposition Author(s): Cioci, G., Mitchell, E., Gautier, C., Wimmerova, M., Perez, S., Gilboa-Garber, N., Imberty, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.187 (Depositor)
R-Value Work:
0.154 (Depositor)
R-Value Observed:
0.156 (Depositor)

Starting Model: other
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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

Structural Basis of Calcium and Galactose Recognition by the Lectin Pa-Il of Pseudomonas Aeruginosa

Cioci, G., Mitchell, E., Gautier, C., Wimmerova, M., Sudakevitz, D., Perez, S., Gilboa-Garber, N., Imberty, A.

(2003) FEBS Lett 555: 297

PubMed: 14644431 Search on PubMed
DOI: https://doi.org/10.1016/s0014-5793(03)01249-3
Primary Citation Related Structures:
1OKO, 1UOJ

PubMed Abstract:
The structure of the tetrameric Pseudomonas aeruginosa lectin I (PA-IL) in complex with galactose and calcium was determined at 1.6 A resolution, and the native protein was solved at 2.4 A resolution. Each monomer adopts a beta-sandwich fold with ligand binding site at the apex. All galactose hydroxyl groups, except O1, are involved in a hydrogen bond network with the protein and O3 and O4 also participate in the co-ordination of the calcium ion. The stereochemistry of calcium galactose binding is reminiscent of that observed in some animal C-type lectins. The structure of the complex provides a framework for future design of anti-bacterial compounds.

Organizational Affiliation

CERMAV-CNRS (affiliated with Université Joseph Fourier), PO Box 53, F-38041 Grenoble Cedex 09, France.

Macromolecule Content

Total Structure Weight: 52.91 kDa
Atom Count: 4,272
Modeled Residue Count: 484
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I GALACTOPHILIC LECTIN	A, B, C, D	121	Pseudomonas aeruginosa	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLA Query on GLA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	K [auth B], O [auth C], R [auth D]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D]
GAL Query on GAL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	F [auth A], L [auth B], P [auth C], S [auth D]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	G [auth A], H [auth A], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [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 N [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	E [auth A], J [auth B], N [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
GAL	BindingDB: 1OKO	Kd: 8.75e+4 (nM) from 1 assay(s)
GLA	BindingDB: 1OKO	Kd: min: 8.75e+4, max: 8.80e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.187 (Depositor)
R-Value Work: 0.154 (Depositor)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.057	α = 90
b = 53.275	β = 90
c = 160.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-12-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-12-04
Type: Initial release
Version 1.1: 2015-08-12
Changes: Atomic model, Derived calculations, Other, Version format compliance
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2024-05-01
Changes: Data collection, Database references, Refinement description, Structure summary

1OKO | pdb_00001oko

Crystal structure of Pseudomonas Aeruginosa Lectin 1 complexed with galactose at 1.6 A resolution

Literature

Structural Basis of Calcium and Galactose Recognition by the Lectin Pa-Il of Pseudomonas Aeruginosa

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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