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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

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 Search on PubMed
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.

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

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00760
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01051
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	F [auth A] J [auth B] K [auth B] N [auth C] O [auth C] 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		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain Q [auth C] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D]	G [auth A], H [auth A], Q [auth C], U [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth C] Focus chain U [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C]	E [auth A], L [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C]	I [auth B], M [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain M [auth C] Interactions & Density Focus chain I [auth B] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length ( ? )	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

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Entry History

Deposition Data

Released Date: 2012-08-01

Deposition Author(s):

Menzel, A.

Neumann, P.

Stubbs, M.T.

Revision History (Full details and data files)

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

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4B2B

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

Thermodynamic signatures in macromolecular interactions involving conformational flexibility.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2