4KQR

CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH (5S)-Penicilloic Acid

Structural Biology Knowledgebase: 4KQR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 4KQR

Classification: Biosynthetic Protein / Antibiotic

Total Structure Weight: 124591.03

Macromolecule Entities
Molecule Chains Length Organism Details
Penicillin-binding protein 3 A, B 564 Pseudomonas aeruginosa Gene Name(s): ftsI PA4418
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
VPP
Query on VPP

A, B (2S,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl- 2,3-dioxopiperazin-1-yl)carbonyl]amino}-2- phenylacetyl]amino}methyl]-5,5-dimethyl-1,3- thiazolidine-4-carboxylic acid
(5S)-Penicilloic Acid (Synonym)
C23 H29 N5 O8 S
OKSUEATVFIVTFV-AESZEHBQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, B IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VPP N/A in BindingDB
IC50: 126000 nM  BindingMOAD
IC50: 126000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.185
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.20 α = 70.77
b = 75.45 β = 85.40
c = 83.22 γ = 85.06

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-15
  • Released Date: 2013-11-06
  • Deposition author(s): Nettleship, J.E., Stuart, D.I., Owens, R.J., Ren, J.

Revision History

No revisions since initial release