1APV

CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES

Structural Biology Knowledgebase: 1APV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.131

Literature

Macromolecules
Sequence Display for 1APV

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 34491.18

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
INHIBITOR ISOVALERYL (IVA)-VAL-VAL-HYDRATED DIFLUOROSTATONE-N-METHYLAMINE I 5 synthetic Details: TRANSITION STATE MIMIC

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

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

E XYLOPYRANOSE
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-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)
DMF
Query on DMF

I DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
IVA
Query on IVA
I NON-POLYMER C5 H10 O2 --
DFO
Query on DFO
I L-PEPTIDE LINKING C8 H15 F2 N O4 --
NME
Query on NME
I NON-POLYMER C H5 N --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.131
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 97.52 α = 90.00
b = 46.57 β = 116.03
c = 66.23 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1991-12-16
  • Released Date: 1994-01-31
  • Deposition author(s): Sielecki, A.R., James, M.N.G.

Revision History

  • 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
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords