Chlorine in PDB 4jk5: Human Urokinase-Type Plasminogen Activator (Upa) in Complex with A Bicyclic Peptide Inhibitor (UK18-D-Ser)

All present enzymatic activity of Human Urokinase-Type Plasminogen Activator (Upa) in Complex with A Bicyclic Peptide Inhibitor (UK18-D-Ser):
3.4.21.73;

The structure of Human Urokinase-Type Plasminogen Activator (Upa) in Complex with A Bicyclic Peptide Inhibitor (UK18-D-Ser), PDB code: 4jk5 was solved by S.A.Buth, P.G.Leiman, S.Chen, C.Heinis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.09 / 1.55
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	121.239, 121.239, 42.631, 90.00, 90.00, 120.00
R / Rfree (%)	14.2 / 21.3

The binding sites of Chlorine atom in the Human Urokinase-Type Plasminogen Activator (Upa) in Complex with A Bicyclic Peptide Inhibitor (UK18-D-Ser) (pdb code 4jk5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human Urokinase-Type Plasminogen Activator (Upa) in Complex with A Bicyclic Peptide Inhibitor (UK18-D-Ser), PDB code: 4jk5:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human Urokinase-Type Plasminogen Activator (Upa) in Complex with A Bicyclic Peptide Inhibitor (UK18-D-Ser)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Urokinase-Type Plasminogen Activator (Upa) in Complex with A Bicyclic Peptide Inhibitor (UK18-D-Ser) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:58.9 occ:0.80 NE1 A:TRP237 3.0 41.1 1.0 N A:LYS92 3.2 42.8 1.0 O A:LEU90 3.4 32.7 1.0 CG A:LYS92 3.6 66.3 1.0 CD A:LYS92 3.7 72.0 1.0 CA A:HIS91 3.7 31.3 1.0 CB A:LYS92 3.7 53.1 1.0 C A:HIS91 3.9 36.1 1.0 CE2 A:TRP237 4.0 43.3 1.0 NE2 A:HIS241 4.0 52.4 1.0 CE1 A:HIS241 4.0 65.7 1.0 CD1 A:TRP237 4.0 40.0 1.0 O A:HOH435 4.0 48.0 1.0 CA A:LYS92 4.1 45.5 1.0 CZ2 A:TRP237 4.2 40.9 1.0 ND1 A:HIS91 4.3 41.6 1.0 C A:LEU90 4.4 30.5 1.0 CG A:HIS91 4.4 40.6 1.0 O A:HOH478 4.4 54.7 1.0 N A:HIS91 4.5 31.3 1.0 CD2 A:HIS91 4.6 32.3 1.0 CE1 A:HIS91 4.6 51.1 1.0 CB A:HIS91 4.7 33.8 1.0 NE2 A:HIS91 4.8 36.0 1.0 CE A:LYS92 4.9 64.3 1.0 NZ A:LYS92 4.9 66.5 1.0

Chlorine binding site 2 out of 2 in the Human Urokinase-Type Plasminogen Activator (Upa) in Complex with A Bicyclic Peptide Inhibitor (UK18-D-Ser)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Urokinase-Type Plasminogen Activator (Upa) in Complex with A Bicyclic Peptide Inhibitor (UK18-D-Ser) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl306 b:61.0 occ:1.00 N A:GLY37B 2.8 67.8 1.0 CA A:GLY37B 2.9 64.7 1.0 OG A:SER37D 3.2 59.4 1.0 C A:GLY37B 3.6 72.9 1.0 N A:GLY37C 3.8 68.2 1.0 N A:SER37D 3.8 49.0 1.0 OH B:TYR5 3.8 75.2 1.0 CB A:SER37D 3.8 48.5 1.0 CB A:HIS37 3.9 50.9 1.0 C A:ARG37A 4.0 68.9 1.0 CG A:ARG37A 4.1 88.8 1.0 C A:HIS37 4.4 56.6 1.0 CA A:SER37D 4.4 49.8 1.0 N A:ARG37A 4.5 54.8 1.0 O A:GLY37B 4.5 66.4 1.0 CA A:ARG37A 4.6 75.8 1.0 CE1 B:TYR5 4.6 51.2 1.0 O A:HIS37 4.7 52.6 1.0 CZ B:TYR5 4.7 56.5 1.0 CA A:HIS37 4.8 50.8 1.0 C A:GLY37C 4.8 66.1 1.0 CA A:GLY37C 4.9 68.8 1.0 CB A:ARG37A 4.9 78.8 1.0 CG A:HIS37 4.9 37.2 1.0 O A:ARG37A 5.0 97.8 1.0

S.Chen, D.Gfeller, S.A.Buth, O.Michielin, P.G.Leiman, C.Heinis. Improving Binding Affinity and Stability of Peptide Ligands By Substituting Glycines with D-Amino Acids. Chembiochem V. 14 1316 2013.
ISSN: ISSN 1439-4227
PubMed: 23828687
DOI: 10.1002/CBIC.201300228