1PML

KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES

DOI: 10.2210/pdb1PML/pdb

Classification: HYDROLASE(SERINE PROTEASE)
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 1994-04-25 Released: 1994-06-22
Deposition Author(s): Padmanabhan, K., Tulinsky, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Observed: 0.145

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Kringle-kringle interactions in multimer kringle structures.

Padmanabhan, K., Wu, T.P., Ravichandran, K.G., Tulinsky, A.

(1994) Protein Sci 3: 898-910

PubMed: 8069221 Search on PubMedSearch on PubMed Central
DOI: 10.1002/pro.5560030605
Primary Citation of Related Structures:
1PML, 1PMK

PubMed Abstract:

The crystal structure of a monoclinic form of human plasminogen kringle 4 (PGK4) has been solved by molecular replacement using the orthorthombic structure as a model and it has been refined by restrained least-squares methods to an R factor of 16.4% at 2.25 A resolution. The X-PLOR structure of kringle 2 of tissue plasminogen activator (t-PAK2) has been refined further using PROFFT (R = 14.5% at 2.38 A resolution). The PGK4 structure has 2 and t-PAK2 has 3 independent molecules in the asymmetric unit. There are 5 different noncrystallographic symmetry "dimers" in PGK4. Three make extensive kringle-kringle interactions related by noncrystallographic 2(1) screw axes without blocking the lysine binding site. Such associations may occur in multikringle structures such as prothrombin, hepatocyte growth factor, plasminogen (PG), and apolipoprotein [a]. The t-PAK2 structure also has noncrystallographic screw symmetry (3(1)) and mimics fibrin binding mode by having lysine of one molecule interacting electrostatically with the lysine binding site of another kringle. This ligand-like binding interaction may be important in kringle-kringle interactions involving non-lysine binding kringles with lysine or pseudo-lysine binding sites. Electrostatic intermolecular interactions involving the lysine binding site are also found in the crystal structures of PGK1 and orthorhombic PGK4. Anions associate with the cationic centers of these and t-PAK2 that appear to be more than occasional components of lysine binding site regions.

Related Citations:

Crystal Structure of the Kringle 2 Domain of Tissue Plasminogen Activator at 2.4 A Resolution
De Vos, A.M., Ultsch, M.H., Kelly, R.F., Padmanabhan, K., Tulinsky, A., Westbrook, M.L., Kossiakoff, A.A.
(1992) Biochemistry 31: 270

Crystal and Molecular Structure of Human Plasminogen Kringle 4 Refined to 1.9A Resolution
Mulichak, A.M., Tulinsky, A., Ravichandran, K.G.
(1991) Biochemistry 30: 10576

The Refined Structure of the Epsilon-Aminocaproic Acid Complex of Human Plasminogen Kringle 4
Wu, T.-P., Padmanabhan, K., Tulinsky, A., Mulichak, A.M.
(1991) Biochemistry 30: 10589

Organizational Affiliation:

Department of Chemistry, Michigan State University, East Lansing 48824.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TISSUE PLASMINOGEN ACTIVATOR KRINGLE 2	A, B, C	86	Homo sapiens	Mutation(s): 0 Gene Names: PLAT EC: 3.4.21.68
Find proteins for P00750 (Homo sapiens) Explore P00750 Go to UniProtKB: P00750
NIH Common Fund Data Resources
PHAROS P00750 GTEx ENSG00000104368
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [B] SDF format, chain F [C] MOL2 format, chain D [A] MOL2 format, chain E [B] MOL2 format, chain F [C]	A, B, C	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction