1PI5

Structure of N289A mutant of AmpC in complex with SM2, carboxyphenylglycylboronic acid bearing the cephalothin R1 side chain

Structural Biology Knowledgebase: 1PI5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 1PI5

Classification: hydrolase

Total Structure Weight: 80221.23

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-lactamase A, B 358 Escherichia coli EC#: 3.5.2.6 IUBMB
Fragment: AmpC
Mutation: N289A
Gene Name(s): ampC ampA b4150 JW4111
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SM2
Query on SM2

A, B (1R)-1-(2-THIENYLACETYLAMINO)-1-(3-CARBOXYPHENYL)METHYLBORONIC ACID
C14 H14 B N O5 S
HQLQTGGLHBYZSA-ZDUSSCGKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SM2 N/A in BindingDB
Ki: 17 nM  BindingMOAD
Ki: 17 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.155
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 119.05 α = 90.00
b = 76.01 β = 115.54
c = 97.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-29
  • Released Date: 2004-02-24
  • Deposition author(s): Roth, T.A., Minasov, G., Focia, P.J., Shoichet, B.K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4