2WEC | pdb_00002wec

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

• PDB DOI: https://doi.org/10.2210/pdb2WEC/pdb
• Entry: 2WEC supersedes: 1WEC

• Classification: HYDROLASE
• Organism(s): Penicillium janthinellum
• Mutation(s): No 


• Deposited: 1998-02-03 Released: 1998-05-27 
• Deposition Author(s): Ding, J., Fraser, M.E., James, M.N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.200 (Depositor) 
• R-Value Work: 
  0.141 (Depositor) 
• R-Value Observed: 
  0.147 (Depositor) 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.46 kDa 
• Atom Count: 2,777 
• Modeled Residue Count: 323 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PENICILLOPEPSIN	A	323	Penicillium janthinellum	Mutation(s): 0  EC: 3.4.23.20
UniProt
Find proteins for P00798 (Penicillium janthinellum) Explore P00798  Go to UniProtKB:  P00798
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PP5	E [auth A]	METHYL (2S)-[1-((N-(NAPHTHALENEACETYL))-L-VALYL)AMINOMETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYL PROPANOATE C28 H32 N2 O7 P AYDPZCGMCQBSDG-AHWVRZQESA-M
MAN	B [auth A], C [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.200 (Depositor) 
• R-Value Work:  0.141 (Depositor) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.24	α = 90
b = 46.63	β = 115.94
c = 65.87	γ = 90

Software Package:

Software Name	Purpose
XENGEN	data collection
XENGEN	data reduction
X-PLOR	model building
TNT	refinement
X-PLOR	refinement
XENGEN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-27 
Deposition Author(s): Ding, J., Fraser, M.E., James, M.N.G.
• This entry supersedes: 1WEC

Revision History  

• Version 1.0: 1998-05-27
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection, Other
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Structure summary