3ZDV

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy- alpha-D-mannopyranoside

Structural Biology Knowledgebase: 3ZDV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.145
  • R-Value Work: 0.115

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZDV

Classification: SUGAR BINDING PROTEIN

Total Structure Weight: 49608.73

Macromolecule Entities
Molecule Chains Length Organism Details
FUCOSE-BINDING LECTIN PA-IIL A, B, C, D 115 Pseudomonas aeruginosa Gene Name(s): lecB PA3361

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
F1A
Query on F1A

A, B, C, D 2,4,6-trimethylbenzenesulfonamide
C9 H13 N O2 S
YECJUZIGFPJWGQ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MMA
Query on MMA

A, B, C, D O1-METHYL-MANNOSE
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.145
  • R-Value Work: 0.115
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.53 α = 90.00
b = 76.98 β = 90.00
c = 99.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-30
  • Released Date: 2013-09-18
  • Deposition author(s): Hauck, D., Joachim, I., Frommeyer, B., Varrot, A., Philipp, B., MOller, H.M., Imberty, A., Exner, T.E., Titz, A.

Revision History

  • 2013-11-13
    Type: Other | Details: MTRIX2, MTRIX3, MTRIX1