PDBsum entry 1krn

Serine protease

PDB id: 1krn

Contents

Protein chain

79 a.a. *

Ligands

SO4

Waters ×249

* Residue conservation analysis

PDB id:

1krn

Name:

Serine protease

Title:

Structure of kringle 4 at 4c temperature and 1.67 angstroms resolution

Structure:

Plasminogen. Chain: a. Fragment: kringle 4 domain. Ec: 3.4.21.7

Source:

Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood

Resolution:

1.67Å R-factor: 0.147 R-free: 0.232

Authors:

B.Stec,M.M.Teeter,M.Whitlow,A.Yamano

Key ref:

B.Stec et al. (1997). Structure of human plasminogen kringle 4 at 1.68 a and 277 K. A possible structural role of disordered residues. Acta Crystallogr D Biol Crystallogr, 53, 169-178. PubMed id: 15299951 DOI: 10.1107/S0907444996012267

Date:

21-Jun-95 Release date: 11-Jan-97

Protein chain

P00747  (PLMN_HUMAN) -  Plasminogen from Homo sapiens

Seq: 810 a.a.

Struc: 79 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.7 - plasmin.
• Reaction: Preferential cleavage: Lys-|-Xaa > Arg-|-Xaa; higher selectivity than trypsin. Converts fibrin into soluble products.

DOI no: 10.1107/S0907444996012267

Acta Crystallogr D Biol Crystallogr 53:169-178 (1997)

PubMed id: 15299951

Structure of human plasminogen kringle 4 at 1.68 a and 277 K. A possible structural role of disordered residues.

B.Stec, A.Yamano, M.Whitlow, M.M.Teeter.

ABSTRACT

Despite considerable effort to elucidate the functional role of the kringle domains, relatively little is known about interactions with other protein domains. Most of the crystal structures describe the interactions at the kringle active site. This study suggests a novel way to interpret structural results such as disorder located away from an active site. The crystal structure of human plasminogen kringle 4 (PGK4) has been refined against 10-1.68 A resolution X-ray data (R(merge) = 3.7%) to the standard crystallographic R = 14.7% using the program X-PLOR. The crystals of PGK4 showed significant instability in cell dimensions (changes more than 1.5 A) even at 277 K. The refinement revealed structural details not observed before [Mulichak, Tulinsky & Ravichandran (1991). Biochemistry, 30, 10576-10588], such as clear density for additional side chains and more extensive disorder. Discrete disorder was detected for residues S73, S78, T80, S89, S91, S92, Ml12, S132, C138 and K142. Most of the disordered residues form two patches on the surface of the protein. This localized disorder suggests that these residues may play a role in quaternary interactions and possibly form an interface with the other domains of proteins that contain kringles, such as plasminogen. Although, an additional residue D65 was refined at the beginning of the sequence, still more residues near the peptide cleavage site must be disordered in the crystal.

Selected figure(s)

Figure 10.
Fig. 10. Bifurcated hydrogen bond of His96NE2. Close contacts are also provided by carbonyl O atoms to the carbon H atoms of the imidazole ring. The 2Fo- Fc electron density is contoured at the 1.5cr level.

Figure 11.
Fig. 11. Trifurcated hydrogen bond of His98 (H98) NE2. The hydrogen bond between Met93 (M93) SD and the carbonyl O atom is also depicted, as are short contacts to CE1.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1997, 53, 169-178) copyright 1997.

Figures were selected by an automated process.