5MAZ | pdb_00005maz

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

PDB DOI: https://doi.org/10.2210/pdb5MAZ/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa UCBPP-PA14
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-11-07 Released: 2017-12-20
Deposition Author(s): Sommer, R., Imberty, A., Titz, A., Varrot, A.
Funding Organization(s): COST

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.142 (Depositor), 0.142 (DCC)
R-Value Work:
0.123 (Depositor), 0.123 (DCC)
R-Value Observed:
0.124 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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.

Macromolecule Content

Total Structure Weight: 48.66 kDa
Atom Count: 4,232
Modeled Residue Count: 456
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin PA-IIL	A, B, C, D	114	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0 Gene Names: lecB, PA14_20610
UniProt
Find proteins for A0A0H2ZE85 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore A0A0H2ZE85 Go to UniProtKB: A0A0H2ZE85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2ZE85
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IGF Query on IGF Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D]	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		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain S [auth D]
FUL Query on FUL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D]	G [auth A], I [auth B], P [auth C], R [auth D]	beta-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-KGJVWPDLSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain P [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain P [auth C] Focus chain R [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	E [auth A] F [auth A] K [auth B] L [auth B] N [auth C] E [auth A], F [auth A], K [auth B], L [auth B], N [auth C], O [auth C], T [auth D], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain T [auth D] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.142 (Depositor), 0.142 (DCC)
R-Value Work: 0.123 (Depositor), 0.123 (DCC)
R-Value Observed: 0.124 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.881	α = 90
b = 49.881	β = 90
c = 288.753	γ = 120

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
COST		COST-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