2JDH

Lectin PA-IIL of P.aeruginosa complexed with disaccharide derivative

PDB DOI: https://doi.org/10.2210/pdb2JDH/pdb

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

Deposited: 2007-01-09 Released: 2007-07-24
Deposition Author(s): Marotte, K., Sabin, C., Preville, C., Pymbock, M., Deguise, I., Wimmerova, M., Mitchell, E.P., Imberty, A., Roy, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.131
R-Value Work: 0.107
R-Value Observed: 0.108

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 49.44 kDa
Atom Count: 4,379
Modelled Residue Count: 456
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUCOSE-BINDING LECTIN PA-IIL	A, B, C, D	115	Pseudomonas aeruginosa	Mutation(s): 0
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYN5 Go to UniProtKB: Q9HYN5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HYN5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G	2		N/A	Interactions Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain E Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G35446HX GlyCosmos: G35446HX GlyGen: G35446HX

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
TA5 Query on TA5 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain R [auth D] SDF format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C]	K [auth B], Q [auth C], R [auth D]	2H-1,2,3-TRIAZOL-4-YLMETHANOL C₃ H₅ N₃ O OADYBXHYXPEGHX-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain Q [auth C] Focus chain R [auth D] Interactions & Density Focus chain K [auth B] Focus chain Q [auth C] Focus chain R [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C]	N [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D]	I [auth A] J [auth A] L [auth B] M [auth B] O [auth C] I [auth A], J [auth A], L [auth B], M [auth B], O [auth C], P [auth C], S [auth D], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.131
R-Value Work: 0.107
R-Value Observed: 0.108
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.552	α = 90
b = 72.829	β = 94.29
c = 54.359	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

Entry History

Deposition Data

Released Date: 2007-07-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-07-24
Type: Initial release
Version 1.1: 2014-02-19
Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

2JDH

Lectin PA-IIL of P.aeruginosa complexed with disaccharide derivative

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)