2PK4
THE REFINED STRUCTURE OF THE EPSILON-AMINOCAPROIC ACID COMPLEX OF HUMAN PLASMINOGEN KRINGLE
Summary for 2PK4
| Entry DOI | 10.2210/pdb2pk4/pdb |
| Descriptor | HUMAN PLASMINOGEN KRINGLE 4, 6-AMINOHEXANOIC ACID (3 entities in total) |
| Functional Keywords | hydrolase(serine protease) |
| Biological source | Homo sapiens (human) |
| Cellular location | Secreted : P00747 |
| Total number of polymer chains | 1 |
| Total formula weight | 9300.28 |
| Authors | Tulinsky, A.,Wu, T.-P. (deposition date: 1991-07-18, release date: 1993-10-31, Last modification date: 2024-10-30) |
| Primary citation | Wu, T.P.,Padmanabhan, K.,Tulinsky, A.,Mulichak, A.M. The refined structure of the epsilon-aminocaproic acid complex of human plasminogen kringle 4. Biochemistry, 30:10589-10594, 1991 Cited by PubMed Abstract: The crystallographic structure of the plasminogen kringle 4-epsilon-aminocaproic acid (ACA) complex (K4-ACA) has been solved by molecular replacement rotation-translation methods utilizing the refined apo-K4 structure as a search model (Mulichak et al., 1991), and it has been refined to an R value of 0.148 at 2.25-A resolution. The K4-ACA structure consists of two interkringle residues, the kringle along with the ACA ligand, and 106 water molecules. The lysine-binding site has been confirmed to be a relatively open and shallow depression, lined by aromatic rings of Trp62, Phe64, and Trp72, which provide a highly nonpolar environment between doubly charged anionic and cationic centers formed by Asp55/Asp57 and Lys35/Arg71. A zwitterionic ACA ligand molecule is held by hydrogen-bonded ion pair interactions and van der Waals contacts between the charged centers. The lysine-binding site of apo-K4 and K4-ACA have been compared: the rms differences in main-chain and side-chain positions are 0.25 and 0.69 A, respectively, both practically within error of the determinations. The largest deviations in the binding site are due to different crystal packing interactions. Thus, the lysine-binding site appears to be preformed, and lysine binding does not require conformational changes of the host. The results of NMR studies of lysine binding with K4 are correlated with the structure of K4-ACA and agree well. PubMed: 1657149DOI: 10.1021/bi00107a030 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.25 Å) |
Structure validation
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