Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history


Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues.

Fraser, M.E.Strynadka, N.C.Bartlett, P.A.Hanson, J.E.James, M.N.

(1992) Biochemistry 31: 5201-5214

  • DOI: 10.1021/bi00137a016
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The molecular structures of three phosphorus-based peptide inhibitors of aspartyl proteinases complexed with penicillopepsin [1, Iva-L-Val-L-Val-StaPOEt [Iva = isovaleryl, StaP = the phosphinic acid analogue of statine [(S)-4-amino-(S)-3-hydroxy-6-me ...

    The molecular structures of three phosphorus-based peptide inhibitors of aspartyl proteinases complexed with penicillopepsin [1, Iva-L-Val-L-Val-StaPOEt [Iva = isovaleryl, StaP = the phosphinic acid analogue of statine [(S)-4-amino-(S)-3-hydroxy-6-methylheptanoic acid] (IvaVVStaPOEt)]; 2, Iva-L-Val-L-Val-L-LeuP-(O)Phe-OMe [LeuP = the phosphinic acid analogue of L-leucine; (O)Phe = L-3-phenyllactic acid; OMe = methyl ester] [Iva VVLP(O)FOMe]; and 3, Cbz-L-Ala-L-Ala-L-LeuP-(O)-Phe-OMe (Cbz = benzyloxycarbonyl) [CbzAALP(O)FOMe]] have been determined by X-ray crystallography and refined to crystallographic agreement factors, R ( = sigma parallel to F0 magnitude of - Fc parallel to/sigma magnitude of F0), of 0.132, 0.131, and 0.134, respectively. These inhibitors were designed to be structural mimics of the tetrahederal transition-state intermediate encountered during aspartic proteinase catalysis. They are potent inhibitors of penicillopepsin with Ki values of 1, 22 nM; 2, 2.8 nM; and 3, 1600 nM, respectively [Bartlett, P. A., Hanson, J. E., & Giannousis, P. P. (1990) J. Org. Chem. 55, 6268-6274]. All three of these phosphorus-based inhibitors bind virtually identically in the active site of penicillopepsin in a manner that closely approximates that expected for the transition state [James, M. N. G., Sielecki, A.R., Hayakawa, K., & Gelb, M. H. (1992) Biochemistry 31, 3872-3886]. The pro-S oxygen atom of the two phosphonate inhibitors and of the phosphinate group of the StaP inhibitor make very short contact distances (approximately 2.4 A) to the carboxyl oxygen atom, O delta 1, of Asp33 on penicillopepsin. We have interpreted this distance and the stereochemical environment of the carboxyl and phosphonate groups in terms of a hydrogen bond that most probably has a symmetric single-well potential energy function. The pro-R oxygen atom is the recipient of a hydrogen bond from the carboxyl group of Asp213. Thus, we are able to assign a neutral status to Asp213 and a partially negatively charged status to Asp33 with reasonable confidence. Similar very short hydrogen bonds involving the active site glutamic acid residues of thermolysin and carboxypeptidase A and the pro-R oxygen of bound phosphonate inhibitors have been reported [Holden, H. M., Tronrud, D. E., Monzingo, A. F., Weaver, L. H., & Matthews, B. W. (1987) Biochemistry 26, 8542-8553; Kim, H., & Lipscomb, W. N. (1991) Biochemistry 30, 8171-8180].(ABSTRACT TRUNCATED AT 400 WORDS)

    Related Citations: 
    • Aspartic Proteinases and Their Catalytic Pathway
      James, M.N.G., Sielecki, A.R.
      (1987) Biological Macromolecules And Assemblies 3: 413
    • Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin
      James, M.N.G., Sielecki, A.R.
      (1985) Biochemistry 24: 3701
    • Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution
      James, M.N.G., Sielecki, A.R.
      (1983) J Mol Biol 163: 299
    • Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin
      James, M.N.G., Sielecki, A., Salituro, F., Rich, D.H., Hofmann, T.
      (1982) Proc Natl Acad Sci U S A 79: 6137
    • The Tertiary Structure of Penicillopepsin. Towards a Catalytic Mechanism for Acid Proteases
      James, M.N.G., Hsu, I-N., Hofmann, T., Sielecki, A.R.
      (1981) Structural Studies On Molecules Of Biologica Interestl --: 350
    • An X-Ray Crystallographic Approach to Enzyme Structure and Function
      James, M.N.G.
      (1980) Can J Biochem 58: 251
    • Structural Evidence for Gene Duplication in the Evolution of the Acid Proteases
      Tang, J., James, M.N.G., Hsu, I.N., Jenkins, J.A., Blundell, T.L.
      (1978) Nature 271: 618
    • Mechanism of Acid Protease Catalysis Based on the Crystal Structure of Penicillopepsin
      James, M.N.G., Hsu, I.-N., Delbaere, L.T.J.
      (1977) Nature 267: 808
    • Penicillopepsin from Penicillium Janthinellum Crystal Structure at 2.8 Angstroms and Sequence Homology with Porcine Pepsin
      Hsu, I.-N., Delbaere, L.T.J., James, M.N.G., Hofmann, T.
      (1977) Nature 266: 140
    • Penicillopepsin. 2.8 Angstroms Structure, Active Site Conformation and Mechanistic Implications
      Hsu, I-N., Delbaere, L.T.J., James, M.N.G., Hofmann, T.
      (1977) Adv Exp Med Biol 95: 61
    • The Crystal Structure of Penicillopepsin at 6 Angstroms Resolution
      Hsu, I-N., Hofmann, T., Nyburg, S.C., James, M.N.G.
      (1976) Biochem Biophys Res Commun 72: 363

    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Canada.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
323Penicillium janthinellumMutation(s): 0 
Find proteins for P00798 (Penicillium janthinellum)
Go to UniProtKB:  P00798
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on 1Z7

Download CCD File 
N-(3-methylbutanoyl)-L-valyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl}-L- valinamide
C30 H50 N3 O8 P
 Ligand Interaction
Query on MAN

Download CCD File 
C6 H12 O6
 Ligand Interaction
Query on XYS

Download CCD File 
C5 H10 O5
 Ligand Interaction
Query on SO4

Download CCD File 
O4 S
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000659 (1Z7)
Query on PRD_000659
EIVA-VAL-VAL-LEU(P)-(O)PHE-OMEPeptide-like /  Inhibitor


External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1Z7Ki:  2.799999952316284   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.5α = 90
b = 46.46β = 115.2
c = 65.93γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2019-07-17
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description