1ce5
From Proteopedia
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|PDB= 1ce5 |SIZE=350|CAPTION= <scene name='initialview01'>1ce5</scene>, resolution 1.90Å | |PDB= 1ce5 |SIZE=350|CAPTION= <scene name='initialview01'>1ce5</scene>, resolution 1.90Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ce5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ce5 OCA], [http://www.ebi.ac.uk/pdbsum/1ce5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ce5 RCSB]</span> | ||
}} | }} | ||
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[[Category: Shah, S S.]] | [[Category: Shah, S S.]] | ||
[[Category: Stroupe, C.]] | [[Category: Stroupe, C.]] | ||
| - | [[Category: BEN]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: CL]] | ||
| - | [[Category: SO4]] | ||
[[Category: hydrolase (serine proteinase)]] | [[Category: hydrolase (serine proteinase)]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:19:50 2008'' |
Revision as of 16:19, 30 March 2008
| |||||||
| , resolution 1.90Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Activity: | Trypsin, with EC number 3.4.21.4 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZAMIDINE
Overview
The relative free energies of binding of trypsin to two amine inhibitors, benzamidine (BZD) and benzylamine (BZA), were calculated using non-Boltzmann thermodynamic integration (NBTI). Comparison of the simulations with the crystal structures of both complexes, trypsin-BZD and trypsin-BZA, shows that NBTI simulations better sample conformational space relative to thermodynamic integration (TI) simulations. The relative binding free energy calculated using NBTI was much closer to the experimentally determined value than that obtained using TI. The error in the TI simulation was found to be primarily due to incorrect sampling of BZA's conformation in the binding pocket. In contrast, NBTI produces a smooth mutation from BZD to BZA using a surrogate potential, resulting in a much closer agreement between the inhibitors' conformations and the omit electron density maps. This superior agreement between experiment and simulation, of both relative binding free energy differences and conformational sampling, demonstrates NBTI's usefulness for free energy calculations in macromolecular simulations.
About this Structure
1CE5 is a Single protein structure of sequence from Bos taurus. Full crystallographic information is available from OCA.
Reference
Non-Boltzmann thermodynamic integration (NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine., Ota N, Stroupe C, Ferreira-da-Silva JM, Shah SA, Mares-Guia M, Brunger AT, Proteins. 1999 Dec 1;37(4):641-53. PMID:10651279
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