1GM9

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.153

Literature

Macromolecules
Sequence Display for 1GM9

Classification: HYDROLASE

Total Structure Weight: 87360.46

Macromolecule Entities
Molecule Chains Length Organism Details
PENICILLIN G ACYLASE ALPHA SUBUNIT A 209 Escherichia coli EC#: 3.5.1.11 IUBMB
Fragment: RESIDUES 27-235
Gene Name(s): pac
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PENICILLIN G ACYLASE BETA SUBUNIT B 557 Escherichia coli EC#: 3.5.1.11 IUBMB
Fragment: RESIDUES 290-846
Gene Name(s): pac

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

B N-[(2S,4S,6R)-2-(DIHYDROXYMETHYL)-4-HYDROXY- 3,3-DIMETHYL-7-OXO-4LAMBDA~4~-THIA-1-AZABICYCLO[3.2.0]HEPT- 6-YL]-2-PHENYLACETAMIDE
OXIDISED PENICILLIN G (Synonym)
C16 H20 N2 O5 S
WMPGEOZLAYOFHH-MBNYWOFBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
SME
Query on SME
A L-PEPTIDE LINKING C5 H11 N O3 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.153
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 51.20 α = 90.00
b = 131.70 β = 105.90
c = 64.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-12
  • Released Date: 2001-11-28
  • Deposition author(s): McVey, C.E., Walsh, M.A., Dodson, G.G., Wilson, K.S., Brannigan, J.A.

Revision History

  • 2013-06-12
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • 2016-12-07
    Type: Database references