PDBsum entry 2ayw

Hydrolase

PDB id: 2ayw

Contents

Protein chain

223 a.a. *

Ligands

1NJ ×2

BEN

MES

GOL

Metals

_CA

Waters ×449

* Residue conservation analysis

PDB id:

2ayw

Name:

Hydrolase

Title:

Crystal structure of the complex formed between trypsin and a designed synthetic highly potent inhibitor in the presence of benzamidine at 0.97 a resolution

Structure:

Cationic trypsin. Chain: a. Synonym: beta-trypsin. Ec: 3.4.21.4

Source:

Bos taurus. Cattle. Organism_taxid: 9913

Resolution:

0.97Å R-factor: 0.138 R-free: 0.157

Authors:

M.Sherawat,P.Kaur,M.Perbandt,C.Betzel,W.A.Slusarchyk,G.S.Bisacchi, C.Chang,B.L.Jacobson,H.M.Einspahr,T.P.Singh

Key ref:

M.Sherawat et al. (2007). Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution. Acta Crystallogr D Biol Crystallogr, 63, 500-507. PubMed id: 17372355 DOI: 10.1107/S090744490700697X

Date:

09-Sep-05 Release date: 17-Jan-06

Protein chain

P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus

Seq: 246 a.a.

Struc: 223 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1107/S090744490700697X

Acta Crystallogr D Biol Crystallogr 63:500-507 (2007)

PubMed id: 17372355

Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution.

M.Sherawat, P.Kaur, M.Perbandt, C.Betzel, W.A.Slusarchyk, G.S.Bisacchi, C.Chang, B.L.Jacobson, H.M.Einspahr, T.P.Singh.

ABSTRACT

The structure of the complex formed between bovine beta-trypsin and the highly potent synthetic inhibitor 2-{3'-[5'-methoxy-2'-(N-p-diaminomethylphenyl)amido]-1'-pyrido}-5-(N-2''-t-butylethanol)amidobenzoic acid (C(28)H(32)N(5)O(6)) has been determined at 0.97 A resolution. X-ray intensity data were collected to 0.97 A under cryocooled conditions. The structure was refined anisotropically using REFMAC5 and SHELX-97 to R(cryst) factors of 13.4 and 12.6% and R(free) factors of 15.7 and 16.3%, respectively. Several regions of the main chain and side chains that have not been previously observed were clearly defined in the present structure. H atoms are indicated as significant peaks in an |F(o) - F(c)| difference map, which accounts for an estimated 35% of all H atoms at the 2.5sigma level. The C, N and O atoms are definitively differentiated in the electron-density maps. The amido part of the inhibitor occupies the specificity pocket and the remainder fills the remaining part of the ligand-binding cleft and interacts with the enzyme through an extensive network of hydrogen bonds. The inhibitor distorts the stereochemistry of the catalytic triad, Ser195-His57-Asp102, thereby blocking the proton-relay process of the active site by preventing the formation of the crucial hydrogen bond between His57 N(delta1) and Asp102 O(delta1).

Selected figure(s)

Figure 1.
Figure 1 The |F[o] - F[c]| map contoured at 2.5 showing the electron densities for two molecules of the inhibitor 2-{3'-[5'-methoxy-2'-(N-p-diaminomethylphenyl)amido]-1'-pyrido}-5-(N-2´´-t-butylethanol)amidobenzoic acid (ONO), benzamidine (BDN), glycerol (GOL) and 2-(N-morpholino)ethanesulfonic acid (MES). ONO1 is shown in yellow, whereas ONO2 is indicated in green. The figure was drawn with PyMOL (DeLano, 2002[DeLano, W. L. (2002). The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.]).

Figure 3.
Figure 3 |2F[o] - F[c]| electron-density map contoured at 1.2 showing disordered residues with more than one conformation for the side chains: (a) Ser37, (b) Asp165, (c) Ser113, (d) Lys60, (e) Arg117.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 500-507) copyright 2007.

Figures were selected by an automated process.