6Q87

Structure of Fucosylated D-antimicrobial peptide SB10 in complex with the Fucose-binding lectin PA-IIL at 2.541 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.541 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.

Baeriswyl, S.Gan, B.H.Siriwardena, T.N.Visini, R.Robadey, M.Javor, S.Stocker, A.Darbre, T.Reymond, J.L.

(2019) Acs Chem.Biol. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fucose-binding lectin
A
114Pseudomonas aeruginosaMutation(s): 0 
Gene Names: lecB
Find proteins for A0A069Q9V4 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A069Q9V4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SB10
B
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NH2
Query on NH2

Download SDF File 
Download CCD File 
B
AMINO GROUP
H2 N
QGZKDVFQNNGYKY-UHFFFAOYAF
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ZDC
Query on ZDC

Download SDF File 
Download CCD File 
B
3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid
C8 H14 O6
YTZUDUWVQZSKNN-OASCRQMUSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
DLY
Query on DLY
B
D-PEPTIDE LINKINGC6 H14 N2 O2

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DLE
Query on DLE
B
D-PEPTIDE LINKINGC6 H13 N O2

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DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

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DTY
Query on DTY
B
D-PEPTIDE LINKINGC9 H11 N O3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.541 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.212 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 130.200α = 90.00
b = 130.200β = 90.00
c = 49.623γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release