PDBsum entry 2wbc

Serine protease inhibitor

PDB id: 2wbc

Contents

Protein chain

183 a.a. *

Waters ×327

* Residue conservation analysis

PDB id:

2wbc

Name:

Serine protease inhibitor

Title:

Refined crystal structure (2.3 angstrom) of a winged bean chymotrypsin inhibitor and location of its second reactive site

Structure:

Chymotrypsin inhibitor. Chain: a. Synonym: wci

Source:

Psophocarpus tetragonolobus. Winged bean. Organism_taxid: 3891. Tissue: seed

Resolution:

2.30Å R-factor: 0.187 R-free: 0.241

Authors:

J.K.Dattagupta,A.Podder,C.Chakrabarti,U.Sen,D.Mukhopadhyay,S.K.Dutta, M.Singh

Key ref:

J.K.Dattagupta et al. (1999). Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site. Proteins, 35, 321-331. PubMed id: 10328267 DOI: 10.1002/(SICI)1097-0134(19990515)35:3<321::AID-PROT6>3.3.CO;2-P

Date:

26-Nov-97 Release date: 25-Feb-98

Protein chain

P10822  (ICW3_PSOTE) -  Chymotrypsin inhibitor 3 from Psophocarpus tetragonolobus

Seq: 207 a.a.

Struc: 183 a.a.

DOI no: 10.1002/(SICI)1097-0134(19990515)35:3<321::AID-PROT6>3.3.CO;2-P

Proteins 35:321-331 (1999)

PubMed id: 10328267

Refined crystal structure (2.3 A) of a double-headed winged bean alpha-chymotrypsin inhibitor and location of its second reactive site.

J.K.Dattagupta, A.Podder, C.Chakrabarti, U.Sen, D.Mukhopadhyay, S.K.Dutta, M.Singh.

ABSTRACT

The crystal structure of a double-headed alpha-chymotrypsin inhibitor, WCI, from winged bean seeds has now been refined at 2.3 A resolution to an R-factor of 18.7% for 9,897 reflections. The crystals belong to the hexagonal space group P6(1)22 with cell parameters a = b = 61.8 A and c = 212.8 A. The final model has a good stereochemistry and a root mean square deviation of 0.011 A and 1.14 degrees from ideality for bond length and bond angles, respectively. A total of 109 ordered solvent molecules were localized in the structure. This improved structure at 2.3 A led to an understanding of the mechanism of inhibition of the protein against alpha-chymotrypsin. An analysis of this higher resolution structure also helped us to predict the location of the second reactive site of the protein, about which no previous biochemical information was available. The inhibitor structure is spherical and has twelve anti-parallel beta-strands with connecting loops arranged in a characteristic beta-trefoil fold common to other homologous serine protease inhibitors in the Kunitz (STI) family as well as to some non homologous functionally unrelated proteins. A wide variation in the surface loop regions is seen in the latter ones.

Selected figure(s)

Figure 5.
Figure 5. The first reactive site of WCI (green) is docked at the enzyme (magenta) active site (van der Waals surface is shown). shows His57 at the center having a hydrophobic environment (partially shown for clarity in viewing).

Figure 8.
Figure 8. The canonical conformation of the second reactive site loop. The side-chain of Glu39 intrudes inside the loop and stabilizes it through hydrogen bonding.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (1999, 35, 321-331) copyright 1999.

Figures were selected by an automated process.