1MPL

CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOG OF A TETRAHEDRAL TRANSITION STATE

Structural Biology Knowledgebase: 1MPL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.140
  • R-Value Work: 0.114

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1MPL

Classification: HYDROLASE

Total Structure Weight: 38221.63

Macromolecule Entities
Molecule Chains Length Organism Details
D-alanyl-D-alanine carboxypeptidase A 349 Streptomyces sp. r61 EC#: 3.4.16.4 IUBMB
Fragment: DD-Peptidase
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
RE1
Query on RE1

A GLYCYL-L-A-AMINOPIMELYL-E-(D-2-AMINOETHYL)PHOSPHONATE
C11 H21 N3 O7 P
DREJXTKPUGMERN-YUMQZZPRSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RE1 N/A in BindingDB
N/A in BindingMoad
Ki: 170000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.140
  • R-Value Work: 0.114
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.90 α = 90.00
b = 66.76 β = 90.00
c = 100.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-09-12
  • Released Date: 2003-02-25
  • Deposition author(s): Silvaggi, N.R., Anderson, J.W., Brinsmade, S.R., Pratt, R.F., Kelly, J.A.

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4