PDBsum entry 1bit

Serine proteinase

PDB id: 1bit

Contents

Protein chain

222 a.a. *

Ligands

SO4

BEN ×2

Metals

_CA

Waters ×125

* Residue conservation analysis

PDB id:

1bit

Name:

Serine proteinase

Title:

The crystal structure of anionic salmon trypsin in a second crystal form

Structure:

Trypsin. Chain: a. Engineered: yes

Source:

Salmo salar. Atlantic salmon. Organism_taxid: 8030

Resolution:

1.83Å R-factor: 0.199

Authors:

G.I.Berglund

Key ref:

G.I.Berglund et al. (1995). Structure of anionic salmon trypsin in a second crystal form. Acta Crystallogr D Biol Crystallogr, 51, 725-730. PubMed id: 15299802 DOI: 10.1107/S0907444995000333

Date:

26-Aug-94 Release date: 01-Nov-94

Protein chain

P35031  (TRY1_SALSA) -  Trypsin-1 from Salmo salar

Seq: 242 a.a.

Struc: 222 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

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

DOI no: 10.1107/S0907444995000333

Acta Crystallogr D Biol Crystallogr 51:725-730 (1995)

PubMed id: 15299802

Structure of anionic salmon trypsin in a second crystal form.

G.I.Berglund, A.O.Smalås, A.Hordvik, N.P.Willassen.

ABSTRACT

Anionic salmon trypsin in a second crystal form (ST-IIB) has been refined at 1.83 A, resolution. The crystals are orthorhombic and belong to space group P2(1)2(1)2 with lattice parameters a = 77.09, b = 82.33 and c = 31.16 A. The present structure has been compared to salmon trypsin as it appears in a previously reported crystal form (ST-IIA) with cell dimensions a = 61.95, b = 84.33 and c = 39.11 A [Smalås & Hordvik (1993). Acta Cryst. D49, 318-330]. The presence of a sulfate group involved in several hydrogen bonds to active-site residues, and the location of an additional benzamidine site in the crystal lattice, are the most striking differences between the present and the previous structure. Superposition of main-chain atoms in the two structures give an overall r.m.s. difference of 0.26 A, with the main differences located to areas with different molecular packing. The overall coordinate error is estimated to be between 0.20 and 0.25 A, by the method of Luzzati.

Selected figure(s)

Figure 3.
Fig. 3. Stereo drawing showing location of the sulfate ion, the two benzamidine molecules and the calcium ion in the three-dimensional structure of ST-lIB. C(~ backbone is drawn wit thin lines while side- chain atoms of the catalytic triad residues (His57, Aspl02, Ser195) and Asp189 at the base of the specificity pocket, the sulfate ion and benzamidne molecules are drawn in thick lines. he calcium ion is indicated by a sphere. ZA246 is in the specficity pocket while BZA247 is located at the surface of the protein mediating contacts to a neighbouring molecule.

Figure 4.
Fig. 4. Stereoview showing density for a benzamidine molecule at two sites. The electron density corresponds to 2Fo-Fc with the benzamidine molecule omitted from the calculations. The maps are contoured at 1.5a level. (a) Benzamidine bound in the specificity pocket of ST-IIB with corresponding hydrogen-bonding pattern. (b) Benzamidine molecule mediating intermolecular contacts at the exten- sion of the primary binding site. Posible hydrogen bonds to Serl71 O and Asn224 N62 are inicated with broken lines. Residues Thr#76 and Phe#82 are from a neighbouring molecule.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1995, 51, 725-730) copyright 1995.

Figures were selected by an automated process.