1GKF

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

Structural Biology Knowledgebase: 1GKF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.148

Literature

Macromolecules
Sequence Display for 1GKF

Classification: HYDROLASE

Total Structure Weight: 92214.06

Macromolecule Entities
Molecule Chains Length Organism Details
PENICILLIN G ACYLASE ALPHA SUBUNIT A 260 Escherichia coli EC#: 3.5.1.11 IUBMB
Fragment: N-TERMINAL NUCLEOPHILE DOMAIN RESIDUES 29-286
Mutation: M16X
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 287-846
Mutation: N241A
Gene Name(s): pac

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

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: 1.41 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.148
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 51.20 α = 90.00
b = 131.70 β = 105.70
c = 63.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-08-13
  • Released Date: 2002-01-04
  • Deposition author(s): McVey, C.E., Walsh, M.A., Dodson, G.G., Wilson, K.S., Brannigan, J.A.

Revision History

  • 2016-12-07
    Type: Polymer description | Details: COMPND
  • 2016-12-07
    Type: Citation | Details: JRNL,REMARK 1
  • 2016-12-07
    Type: Non-polymer description | Details: FORMUL
  • 2016-12-07
    Type: Version format compliance | Details: REMARK 4
  • 2016-12-07
    Type: Function and keywords | Details: KEYWDS
  • 2016-12-07
    Type: Atom nomenclature | Details: ATOM
  • 2016-12-07
    Type: Other | Details: REMARK 465,TER,REMARK 470,REMARK 525,MASTER,HEADER,REMARK 280
  • 2016-12-07
    Type: Biological assembly | Details: REMARK 300,REMARK 350