1MY8

AmpC beta-lactamase in complex with an M.carboxyphenylglycylboronic acid bearing the cephalothin R1 side chain

Structural Biology Knowledgebase: 1MY8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.167

Literature

Macromolecules
Sequence Display for 1MY8

Classification: hydrolase

Total Structure Weight: 79821.92

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

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SM3
Query on SM3

A, B (1R)-1-(2-THIENYLACETYLAMINO)-1-PHENYLMETHYLBORONIC ACID
C13 H14 B N O3 S
LGJCDEZMANATFA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
SM3 N/A in BindingDB
Ki: 35 nM  BindingMOAD
Ki: 35 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.167
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 118.21 α = 90.00
b = 76.70 β = 116.31
c = 97.66 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-03
  • Released Date: 2003-03-04
  • Deposition author(s): Morandi, F., Caselli, E., Morandi, S., Focia, P.J., Blazquez, J., Shoichet, B.K., Prati, F.

Revision History

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