1UHB

Crystal structure of porcine alpha trypsin bound with auto catalyticaly produced native peptide at 2.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1UHB/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2003-06-27 Released: 2004-07-27 
• Deposition Author(s): Pattabhi, V., Syed Ibrahim, B., Shamaladevi, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Trypsin activity reduced by an autocatalytically produced nonapeptide.

Ibrahim, B.S., Shamaladevi, N., Pattabhi, V.

(2004) J Biomol Struct Dyn 21: 737-744

• PubMed: 15106996 
• DOI: https://doi.org/10.1080/07391102.2004.10506964
• Primary Citation of Related Structures:  
  1UHB


• PubMed Abstract: 
  

  Trypsin, a serine protease enzyme plays a pivotal role in digestion and is autocatalytic. The crystal structure of a complex formed between porcine trypsin and an auto catalytically produced peptide is reported here. This complex shows a reduction in enzyme activity as compared to native beta-trypsin. The nonapeptide has a lysine, which is recognized by Asp 189 at the specificity pocket. The auto catalytically produced native nonapeptide is bound at the active site cleft like other trypsin inhibitors but the important interactions with the oxyanion hole are absent. The peptide covers only a part of the active site cleft and hence the enzyme activity is reduced rather than being inhibited.

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Organizational Affiliation: 

Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Guindy, Chennai-600025, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.51 kDa 
• Atom Count: 1,856 
• Modelled Residue Count: 232 
• Deposited Residue Count: 232 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin	A	125	Sus scrofa	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa) Explore P00761  Go to UniProtKB:  P00761

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin	B	98	Sus scrofa	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa) Explore P00761  Go to UniProtKB:  P00761

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
9-mer peptide from Trypsin	C [auth P]	9	Sus scrofa	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa) Explore P00761  Go to UniProtKB:  P00761

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth P]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.945	α = 90
b = 53.921	β = 90
c = 77.245	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
DENZO	data reduction
CNS	refinement
REFMAC	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-07-27 
Deposition Author(s): Pattabhi, V., Syed Ibrahim, B., Shamaladevi, N.

Revision History  

• Version 1.0: 2004-07-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2019-11-06
  Changes: Data collection, Database references
• Version 1.5: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description