1PPG | pdb_00001ppg

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

• PDB DOI: https://doi.org/10.2210/pdb1PPG/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 3391280 
• DOI: https://doi.org/10.1016/0014-5793(88)80118-2
• Primary Citation 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 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.

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Organizational Affiliation: 
• Max-Planck-Institut für Biochemie, Martinsried, FRG.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.67 kDa 
• Atom Count: 2,053 
• Modeled Residue Count: 224 
• Deposited Residue Count: 224 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN LEUKOCYTE ELASTASE	A [auth E]	218	Homo sapiens	Mutation(s): 0  EC: 3.4.21.37
UniProt & NIH Common Fund Data Resources
Find proteins for P08246 (Homo sapiens) Explore P08246  Go to UniProtKB:  P08246
PHAROS:  P08246 GTEx:  ENSG00000197561
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P08246-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MEO-SUCCINYL-ALA-ALA-PRO-VAL CHLOROMETHYLKETONE	B [auth I]	6	N/A	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	C [auth A]	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G61334IA GlyCosmos: G61334IA GlyGen: G61334IA

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	D [auth B]	8		N-Glycosylation
Glycosylation Resources
GlyTouCan: G32078TL GlyCosmos: G32078TL GlyGen: G32078TL

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
VAI	B [auth I]	PEPTIDE-LIKE	C5 H13 N O2		VAL

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000414	B [auth I]	Meo-Suc-Ala-Ala-Pro-Val-chloromethyl ketone	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

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

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.2	α = 90
b = 74.2	β = 90
c = 70.6	γ = 120

Software Package:

Software Name	Purpose
EREF	refinement

Structure Validation

Entry History 

Deposition Data

• 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
• Version 3.0: 2024-07-10
  Changes: Advisory, Data collection, Database references, Polymer sequence, Structure summary