3ZDV

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy-alpha-D-mannopyranoside

PDB DOI: https://doi.org/10.2210/pdb3ZDV/pdb

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

Deposited: 2012-11-30 Released: 2013-09-18
Deposition Author(s): Hauck, D., Joachim, I., Frommeyer, B., Varrot, A., Philipp, B., MOller, H.M., Imberty, A., Exner, T.E., Titz, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.145
R-Value Work: 0.115
R-Value Observed: 0.116

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: 49.61 kDa
Atom Count: 4,025
Modelled Residue Count: 456
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 PAO1	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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F1A Query on F1A Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain V [auth D] SDF format, chain H [auth A] SDF format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain V [auth D] MOL2 format, chain H [auth A] MOL2 format, chain R [auth C]	H [auth A], L [auth B], R [auth C], V [auth D]	2,4,6-trimethylbenzenesulfonamide C₉ H₁₃ N O₂ S YECJUZIGFPJWGQ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain V [auth D]
MMA Query on MMA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D]	G [auth A], K [auth B], Q [auth C], U [auth D]	methyl alpha-D-mannopyranoside C₇ H₁₄ O₆ HOVAGTYPODGVJG-VEIUFWFVSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [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] MOL2 format, chain W [auth D]	W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain W [auth D] Interactions & Density Focus chain W [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain T [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] O [auth C] E [auth A], F [auth A], I [auth B], J [auth B], O [auth C], P [auth C], S [auth D], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [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 E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [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: 1.41 Å
R-Value Free: 0.145
R-Value Work: 0.115
R-Value Observed: 0.116
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.53	α = 90
b = 76.98	β = 90
c = 99.66	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2013-11-13
Changes: Other
Version 1.2: 2017-09-13
Changes: Data collection, 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