1BXO

ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL CYCLO[(2S)-2-[[(1R)-1-(N-(L-N-(3-METHYLBUTANOYL)VALYL-L-ASPARTYL)AMINO)-3-METHYLBUT YL] HYDROXYPHOSPHINYLOXY]-3-(3-AMINOMETHYL) PHENYLPROPANOATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Observed: 0.099

Literature

Macromolecules
Sequence Display for 1BXO

Classification: HYDROLASE

Total Structure Weight: 34748.37

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (PENICILLOPEPSIN) A 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
PP7
Query on PP7

A METHYL CYCLO[(2S)-2-[[(1R)-1-(N-(L-N-(3-METHYLBUTANOYL)VALYL- L-ASPARTYL)AMINO)-3-METHYLBUTYL]HYDROXYPHOSPHINYLOXY]- 3-(3-AMINOMETHYL)PHENYLPROPANOATE
C30 H47 N4 O9 P
BOYAGOIPWLIWCX-IDJLGEMNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PP7 N/A in BindingDB
Ki: 0.1 nM  BindingMOAD
Ki: 0.10 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Observed: 0.099
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 96.98 α = 90.00
b = 46.65 β = 115.57
c = 65.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-10-07
  • Released Date: 1998-10-14
  • Deposition author(s): Khan, A.R., Parrish, J.C., Fraser, M.E., Smith, W.W., Bartlett, P.A., James, M.N.G.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4