Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 26292.76 
• Atom Count: 1685 
• Residue Count: 242 
• Unique protein chains: 1

1UTL

Trypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements

• DOI: 10.2210/pdb1UTL/pdb

• Classification: HYDROLASE
• Organism(s): Salmo salar


• Deposited: 2003-12-09 Released: 2004-01-15 
• Deposition Author(s): Leiros, H.-K.S., Brandsdal, B.O., Andersen, O.A., Os, V., Leiros, I., Helland, R., Otlewski, J., Willassen, N.P., Smalas, A.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 

Literature

Trypsin Specificity as Elucidated by Lie Calculations, X-Ray Structures, and Association Constant Measurements

Leiros, H.-K.S., Brandsdal, B.O., Andersen, O.A., Os, V., Leiros, I., Helland, R., Otlewski, J., Willassen, N.P., Smalas, A.O.

(2004) Protein Sci. 13: 1056

• PubMed: 15044735 
• DOI: 10.1110/ps.03498604
• Primary Citation of Related Structures:  
  1UTM, 1UTQ, 1UTP, 1UTO, 1UTN, 1UTK, 1UTJ


• PubMed Abstract: 
  

The variation in inhibitor specificity for five different amine inhibitors bound to CST, BT, and the cold-adapted AST has been studied by use of association constant measurements, structural analysis of high-resolution crystal structures, and the LIE method. Experimental data show that AST binds the 1BZA and 2BEA inhibitors 0.8 and 0.5 kcal/mole more strongly than BT. However, structural interactions and orientations of the inhibitors within the S1 site have been found to be virtually identical in the three enzymes studied. For example, the four water molecules in the inhibitor-free structures of AST and BT are channeled into similar positions in the S1 site, and the nitrogen atom(s) of the inhibitors are found in two cationic binding sites denoted Position1 and Position2. The hydrophobic binding contributions for all five inhibitors, estimated by the LIE calculations, are also in the same order (-2.1 +/- 0.2 kcal/mole) for all three enzymes. Our hypothesis is therefore that the observed variation in inhibitor binding arises from different electrostatic interactions originating from residues outside the S1 site. This is well illustrated by AST, in which Asp 150 and Glu 221B, despite some distance from the S1 binding site, lower the electrostatic potential of the S1 site and thus enhance substrate binding. Because the trends in the experimentally determined binding energies were reproduced by the LIE calculations after adding the contribution from long-range interactions, we find this method very suitable for rational studies of protein-substrate interactions.

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Organizational Affiliation: 

University of Tromsø, N-9037 Tromsø, Norway.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRYPSIN I	M	242	Salmo salar	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P35031 (Salmo salar) Go to UniProtKB:  P35031

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	M	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
PRA	M	3-PHENYLPROPYLAMINE C9 H14 N LYUQWQRTDLVQGA-UHFFFAOYSA-O
MPD	M	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PRA	Kd: 3412000 nM BINDINGMOAD
PRA	Kd: 3410000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 44.944	α = 90.00
b = 48.269	β = 90.00
c = 83.102	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
SCALA	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-09 
• Released Date: 2004-01-15 
• Deposition Author(s): Leiros, H.-K.S., Brandsdal, B.O., Andersen, O.A., Os, V., Leiros, I., Helland, R., Otlewski, J., Willassen, N.P., Smalas, A.O.

Revision History 

• Version 1.0: 2004-01-15
  Type: Initial release
• Version 1.1: 2011-06-02
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance