2WED

ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE MACROCYCLIC INHIBITOR:METHYL[CYCLO-7[(2R)-((N-VALYL)AMINO)-2-(HYDROXYL-(1S)-1-METHYOXYCARBONYL-2-PHENYLETHOXY)PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE], SODIUM SALT

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PENICILLOPEPSIN323Penicillium janthinellumMutation(s): 0 
EC: 3.4.23.20
UniProt
Find proteins for P00798 (Penicillium janthinellum)
Explore P00798 
Go to UniProtKB:  P00798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00798
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PP6
Query on PP6
Download Ideal Coordinates CCD File 
E [auth A]METHYL[CYCLO-7[(2R)-((N-VALYL)AMINO)-2-(HYDROXYL-(1S)-1-METHYLOXYCARBONYL-2-PHENYLETHOXY)PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE]
C29 H32 N2 O7 P
BJANYCOFDSBOJK-OIKPOIBNSA-M
MAN
Query on MAN
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
PP6 Binding MOAD:  2WED Ki: 800 (nM) from 1 assay(s)
PDBBind:  2WED Ki: 800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.88α = 90
b = 46.64β = 116.14
c = 66.59γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary