5D2A

Bifunctional dendrimers


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.134 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Overcoming antibiotic resistance inPseudomonas aeruginosabiofilms using glycopeptide dendrimers.

Michaud, G.Visini, R.Bergmann, M.Salerno, G.Bosco, R.Gillon, E.Richichi, B.Nativi, C.Imberty, A.Stocker, A.Darbre, T.Reymond, J.L.

(2016) Chem Sci 7: 166-182


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fucose-binding lectin
A, B
114Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: lecB
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HYN5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL
C
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ZDC-ALA-PRO-ALA-LYS-PHE-CYS-ALA-PRO-ALA-PHB-GAL
D, E
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Download SDF File 
Download CCD File 
C
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
PHB
Query on PHB

Download SDF File 
Download CCD File 
C
P-HYDROXYBENZOIC ACID
C7 H6 O3
FJKROLUGYXJWQN-UHFFFAOYSA-N
 Ligand Interaction
ZDC
Query on ZDC

Download SDF File 
Download CCD File 
D, E
3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid
C8 H14 O6
YTZUDUWVQZSKNN-OASCRQMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.134 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 105.107α = 90.00
b = 105.107β = 90.00
c = 111.092γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2018-07-11
    Type: Data collection, Database references