Crystal structure of the NK1 fragment of human hepatocyte growth factor at 2.0 å resolution  Mark Ultsch, Nathalie A Lokker, Paul J Godowski, Abraham M de Vos  Structure  Volume 6, Issue 11, Pages 1383-1393 (November 1998) DOI: 10.1016/S0969-2126(98)00138-5

Figure 1 Backbone structure of NK1. (a) The NK1 dimer found in the asymmetric unit, with one monomer (molecule 1 in the text) in green and the other (molecule 2) in red. Three sulfate ions and two HEPES molecules bound to the dimer are shown in stick rendering. The termini are labeled. (b) Stereoview Cα trace of the NK1 monomer (molecule 1), with the sulfate ions and HEPES molecule included. Every tenth residue is labeled. The orientation in this panel is obtained from panel (a) by a rotation of 180° about the horizontal axis. The MOLSCRIPT [49], RASTER 3D [50] and GRASP [51] programs were used in making the figures. Structure 1998 6, 1383-1393DOI: (10.1016/S0969-2126(98)00138-5)

Figure 2 The binding pocket of the NK1 kringle. Mainchain segments are green, sidechain carbon atoms are in light gray, oxygens are in red and nitrogens in blue. A HEPES molecule bound in the pocket in the crystal structure is shown with its carbon atoms in dark gray and its sulfur atom in yellow. Hydrogen bonds are represented by dashed lines. Structure 1998 6, 1383-1393DOI: (10.1016/S0969-2126(98)00138-5)

Figure 3 Sequence alignments, with the secondary structure elements observed in NK1 shown at the top. (a) N domains and β strands are labeled as described in the text. Positively charged residues discussed in the text are in blue, residues in the intramolecular interface are underlined and residues in the intermolecular interface are overlined. MSP, macrophage stimulating protein (human); PL, plasminogen (human). (b) Kringle domains. Residues colored red are the proposed receptor-binding determinants of NK1; underlined and overlined residues as in (a). Structure 1998 6, 1383-1393DOI: (10.1016/S0969-2126(98)00138-5)

Figure 4 Stereoview of the intramolecular interface between the N domain (green) and the kringle domain (yellow) around the salt bridge between Lys43 and Asp171. Water molecules are shown as red spheres, and hydrogen bonds are represented by dashed lines. Structure 1998 6, 1383-1393DOI: (10.1016/S0969-2126(98)00138-5)

Figure 5 Stereoview of the environment of the N domain Asp117. Structure 1998 6, 1383-1393DOI: (10.1016/S0969-2126(98)00138-5)

Figure 6 Putative heparin-binding patches of NK1. (a) Surface renderings of NK1 (left) and our NK2 model (center), with a ribbon rendering of NK2 to show the orientation (right). Patches 1 and 2 (see text) are labeled, as are Arg93 and Lys94. (b) Same as (a), but rotated by approximately 90° about the vertical axis. A large, positively charged groove is delineated by the white contour. The solvent-accessible surfaces are color coded for charge (blue is positive). Sulfate ions are shown in yellow and red, and rendered as van der Waals spheres (left and center) or sticks (right). In the surface renderings the bound HEPES molecule is shown as a green patch. Structure 1998 6, 1383-1393DOI: (10.1016/S0969-2126(98)00138-5)