1PPM

CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES

Structural Biology Knowledgebase: 1PPM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Observed: 0.150

Literature

Macromolecules
Sequence Display for 1PPM

Classification: HYDROLASE / hydrolase inhibitor

Total Structure Weight: 34501.08

Macromolecule Entities
Molecule Chains Length Organism Details
PENICILLOPEPSIN E 323 Penicillium janthinellum EC#: 3.4.23.20 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0P1
Query on 0P1

E N-[(benzyloxy)carbonyl]-L-alanyl-N-{(1S)- 1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]- 3-methylbutyl}-L-alaninamide
Cbz-Ala-Ala-Leu(P)-(O)-Phe-OMe (Synonym)
C29 H40 N3 O9 P
VWCUANLUSQBJLX-WIHVIGOGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

E ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ARA
Query on ARA

E ALPHA-L-ARABINOSE
C5 H10 O5
SRBFZHDQGSBBOR-QMKXCQHVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

E SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0P1 N/A in BindingDB
Ki: 1600 nM  BindingMOAD
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000328
Query on PRD_000328
E Cbz-Ala-Ala-Leu(P)-(O)-Phe-OMe Peptide-like /
Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Observed: 0.150
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 97.40 α = 90.00
b = 46.59 β = 115.70
c = 66.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1992-06-01
  • Released Date: 1993-10-31
  • Deposition author(s): Fraser, M.E., James, M.N.G.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description