2WEC

ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL(2S)-[1-(((N-(1-NAPHTHALENEACETYL))-L-VALYL)AMINOMETHYL)HYDROXY PHOSPHINYLOXY]-3-PHENYLPROPANOATE, SODIUM SALT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Macrocyclic Inhibitors of Penicillopepsin. II. X-Ray Crystallographic Analyses of Penicillopepsin Complexed with a P3-P1 Macrocyclic Peptidyl Inhibitor and with its Two Acyclic Analogues

Ding, J.Fraser, M.E.Meyer, J.H.Bartlett, P.A.James, M.N.G.

(1998) J.Am.Chem.Soc. 120: 4610-4621


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PENICILLOPEPSIN
A
323Penicillium janthinellumMutation(s): 0 
EC: 3.4.23.20
Find proteins for P00798 (Penicillium janthinellum)
Go to UniProtKB:  P00798
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PP5
Query on PP5

Download SDF File 
Download CCD File 
A
METHYL (2S)-[1-((N-(NAPHTHALENEACETYL))-L-VALYL)AMINOMETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYL PROPANOATE
C28 H32 N2 O7 P
AYDPZCGMCQBSDG-AHWVRZQESA-M
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PP5Ki: 110000 nM BINDINGMOAD
PP5Ki: 110000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.141 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.240α = 90.00
b = 46.630β = 115.94
c = 65.870γ = 90.00
Software Package:
Software NamePurpose
XENGENdata collection
TNTrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection, Other