5MAZ

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 3-Thiophenesulfonamide-2,5-dimethyl-N-methyl-beta-L-fucopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IGFClick on this verticalbar to view detailsBest fitted FULClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Discovery of a new class of C-glycoside based inhibitors of the virulence factor LecB from Pseudomonas aeruginosa

Sommer, R.Wagner, S.Varrot, A.Hauk, D.Ryckmans, T.Hartman, R.W.Brunner, T.Rademacher, C.Imberty, A.Titz, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucose-binding lectin PA-IIL
A, B, C, D
114Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: lecBPA14_20610
UniProt
Find proteins for A0A0H2ZE85 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZE85 
Go to UniProtKB:  A0A0H2ZE85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZE85
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IGF
Query on IGF

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
Q [auth C],
S [auth D]
N,2,5-trimethyl-3-thiophenesulfonamide
C7 H11 N O2 S2
MQZNMDAQVFXGMG-UHFFFAOYSA-N
FUL
Query on FUL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
P [auth C],
R [auth D]
beta-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
V [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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M [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth B]
N [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.881α = 90
b = 49.881β = 90
c = 288.753γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IGFClick on this verticalbar to view detailsBest fitted FULClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
COSTCOST-STSM-ECOST-STSM-BM1003-240314-042549

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary