6Y0W | pdb_00006y0w

Fucosylated antimicrobial linear peptide cFucRH46D in complex with the fucose binding lectin LecB from Pseudomonas aeruginosa at 2.1 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6Y0W/pdb

Classification: ANTIBIOTIC
Organism(s): Pseudomonas aeruginosa, synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-02-10 Released: 2021-02-17
Deposition Author(s): Baeriswyl, S., Stocker, A., Reymond, J.-L.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.222 (Depositor), 0.193 (DCC)
R-Value Work:
0.175 (Depositor), 0.189 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Fucosylated antimicrobial linear peptide cFucRH46D in complex with the fucose binding lectin LecB from Pseudomonas aeruginosa at 2.1 Angstrom resolution

Baeriswyl, S., Stocker, A., Reymond, J.-L.

To be published.

Macromolecule Content

Total Structure Weight: 27.69 kDa
Atom Count: 2,017
Modeled Residue Count: 256
Deposited Residue Count: 258
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin	A, C [auth B]	115	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070... lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HYN5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cFucRH46D	B [auth C], D	14	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZDC (Subject of Investigation/LOI) Query on ZDC Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain G [auth C] MOL2 format, chain J [auth D] MOL2 format, chain G [auth C] mmCIF format, chain J [auth D] mmCIF format, chain G [auth C]	G [auth C], J [auth D]	3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid C₈ H₁₄ O₆ YTZUDUWVQZSKNN-OASCRQMUSA-N		Interactions Focus chain G [auth C] Focus chain J [auth D] Interactions & Density Focus chain G [auth C] Focus chain J [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]

Modified Residues 7 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL Query on DAL	B [auth C], D	D-PEPTIDE LINKING	C₃ H₇ N O₂		Not Available
DHI Query on DHI	B [auth C], D	D-PEPTIDE LINKING	C₆ H₁₀ N₃ O₂		Not Available
DLE Query on DLE	B [auth C], D	D-PEPTIDE LINKING	C₆ H₁₃ N O₂		Not Available
DLY Query on DLY	B [auth C], D	D-PEPTIDE LINKING	C₆ H₁₄ N₂ O₂		Not Available
DPN Query on DPN	B [auth C], D	D-PEPTIDE LINKING	C₉ H₁₁ N O₂		Not Available
DTR Query on DTR	B [auth C], D	D-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₂		Not Available
DTY Query on DTY	B [auth C], D	D-PEPTIDE LINKING	C₉ H₁₁ N O₃		Not Available

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.222 (Depositor), 0.193 (DCC)
R-Value Work: 0.175 (Depositor), 0.189 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.999	α = 90
b = 68.999	β = 90
c = 271.453	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2021-02-17
Type: Initial release
Version 1.1: 2022-12-07
Changes: Database references
Version 1.2: 2024-01-31
Changes: Data collection, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.