4B2B

Structure of the factor Xa-like trypsin variant triple-Ala (TGPA) in complex with eglin C

• PDB DOI: https://doi.org/10.2210/pdb4B2B/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Bos taurus, Hirudo medicinalis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-07-13 Released: 2012-08-01 
• Deposition Author(s): Menzel, A., Neumann, P., Stubbs, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.204 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Thermodynamic signatures in macromolecular interactions involving conformational flexibility.

Menzel, A., Neumann, P., Schwieger, C., Stubbs, M.T.

(2014) Biol Chem 395: 905-911

• PubMed: 25003391 
• DOI: https://doi.org/10.1515/hsz-2014-0177
• Primary Citation of Related Structures:  
  4B1T, 4B2A, 4B2B, 4B2C


• PubMed Abstract: 
  

  The energetics of macromolecular interactions are complex, particularly where protein flexibility is involved. Exploiting serendipitous differences in the plasticity of a series of closely related trypsin variants, we analyzed the enthalpic and entropic contributions accompanying interaction with L45K-eglin C. Binding of the four variants show significant differences in released heat, although the affinities vary little, in accordance with the principle of enthalpy-entropy compensation. Binding of the most disordered variant is almost entirely enthalpically driven, with practically no entropy change. As structures of the complexes reveal negligible differences in protein-inhibitor contacts, we conclude that solvent effects contribute significantly to binding affinities.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.45 kDa 
• Atom Count: 5,099 
• Modelled Residue Count: 588 
• Deposited Residue Count: 588 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATIONIC TRYPSIN	A, C	223	Bos taurus	Mutation(s): 8  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EGLIN C	B, D	71	Hirudo medicinalis	Mutation(s): 1
UniProt
Find proteins for P01051 (Hirudo medicinalis) Explore P01051  Go to UniProtKB:  P01051

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], J [auth B], K [auth B], N [auth C], O [auth C], P [auth C], R [auth D], S [auth D], T [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], Q [auth C], U [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	E [auth A], L [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	I [auth B], M [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.204 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.34	α = 90
b = 36.94	β = 103.41
c = 103.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Menzel, A., Neumann, P., Stubbs, M.T.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Database references
• Version 1.2: 2014-07-16
  Changes: Database references
• Version 1.3: 2014-07-23
  Changes: Database references
• Version 1.4: 2019-05-08
  Changes: Data collection, Database references, Experimental preparation, Other
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.6: 2024-11-20
  Changes: Structure summary