1PPG

The refined 2.3 angstroms crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report



Literature

The refined 2.3 A crystal structure of human leukocyte elastase in a complex with a valine chloromethyl ketone inhibitor.

Wei, A.Z.Mayr, I.Bode, W.

(1988) FEBS Lett 234: 367-373

  • DOI: 10.1016/0014-5793(88)80118-2
  • Primary Citation of Related Structures:  
    1PPG

  • PubMed Abstract: 
  • The stoichiometric complex formed between human leukocyte elastase and a synthetic MeO-Suc-Ala-Ala-Pro-Val chloromethyl ketone inhibitor was co-crystallized and its X-ray structure determined, using Patterson search methods. Its structure has been cr ...

    The stoichiometric complex formed between human leukocyte elastase and a synthetic MeO-Suc-Ala-Ala-Pro-Val chloromethyl ketone inhibitor was co-crystallized and its X-ray structure determined, using Patterson search methods. Its structure has been crystallographically refined to a final R value of 0.145 (8.0 and 2.3 A). The enzyme structure is very similar to that recently observed in a complex formed with the ovomucoid third domain from turkey [(1986) EMBO J. 5,2453-2458]. The rms deviation of all alpha-carbon atoms is 0.32 A. The peptidic inhibitor is bound in a similar overall conformation as the ovomucoid binding segment. Covalent bonds are formed between Val-P1 of the inhibitor and His-57 NE2 and Ser-195 OG of the enzyme. The carbonyl carbon is tetrahedrally deformed to a hemiketal. The valine side chain is arranged in the S1 pocket in the g-conformation.


    Related Citations: 
    • X-Ray Crystal Structure of the Complex of Human Leukocyte Elastase (Pmn Elastase) and the Third Domain of the Turkey Ovomucoid Inhibitor
      Bode, W., Wei, A.-Z., Huber, R., Meyer, E., Travis, J., Neumann, S.
      (1986) EMBO J 5: 2453

    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, FRG.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN LEUKOCYTE ELASTASEE218Homo sapiensMutation(s): 0 
Gene Names: ELANEELA2
EC: 3.4.21.37
Find proteins for P08246 (Homo sapiens)
Explore P08246 
Go to UniProtKB:  P08246
NIH Common Fund Data Resources
PHAROS  P08246
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONEI6N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
A
8 N-Glycosylation
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
8 N-Glycosylation
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
VAI
Query on VAI
IPEPTIDE-LIKEC5 H13 N O2VAL
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000414
Query on PRD_000414
IMeo-Suc-Ala-Ala-Pro-Val-chloromethyl ketonePeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.145 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.2α = 90
b = 74.2β = 90
c = 70.6γ = 120
Software Package:
Software NamePurpose
EREFrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1991-10-24 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Bode, W., Wei, A-Z.

Revision History 

  • Version 1.0: 1994-01-31
    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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary