Chlorine in PDB 6umu: Human Apo Pd-1 Triple Mutant

The structure of Human Apo Pd-1 Triple Mutant, PDB code: 6umu was solved by S.Tang, P.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.49 / 1.18
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.172, 46.172, 89.270, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 16.4

The binding sites of Chlorine atom in the Human Apo Pd-1 Triple Mutant (pdb code 6umu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human Apo Pd-1 Triple Mutant, PDB code: 6umu:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Human Apo Pd-1 Triple Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Apo Pd-1 Triple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:24.3 occ:1.00 N A:LEU138 3.2 13.5 1.0 N A:PHE37 3.3 14.4 1.0 O A:HOH321 3.4 26.3 1.0 CA A:THR36 3.5 16.4 1.0 CB A:LEU138 3.6 15.8 1.0 CB A:SER137 3.9 13.1 1.0 C A:THR36 3.9 15.2 1.0 CG A:LEU138 3.9 17.1 1.0 CB A:THR36 3.9 20.8 1.0 CA A:LEU138 4.0 14.2 1.0 O A:PHE37 4.1 17.7 1.0 CA A:SER137 4.2 13.8 1.0 C A:SER137 4.2 13.5 1.0 O A:LEU138 4.2 14.3 1.0 O A:PRO35 4.2 15.4 1.0 CA A:PHE37 4.3 13.7 1.0 CB A:PHE37 4.4 14.2 1.0 CG2 A:THR36 4.4 20.9 1.0 CD1 A:LEU138 4.4 22.2 1.0 C A:LEU138 4.5 13.4 1.0 O A:HOH364 4.5 44.0 1.0 C A:PHE37 4.6 14.2 1.0 N A:THR36 4.7 15.1 1.0 OG A:SER137 4.7 13.2 1.0 C A:PRO35 4.9 14.7 1.0

Chlorine binding site 2 out of 3 in the Human Apo Pd-1 Triple Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Apo Pd-1 Triple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:31.8 occ:0.43 CL A:CL202 0.0 31.8 0.4 CL A:CL202 2.7 29.0 0.6 O A:HOH387 2.7 20.7 0.6 O A:HOH329 2.8 22.8 1.0 O A:HOH387 3.3 27.6 0.4 N A:GLU84 3.9 19.0 1.0 CD1 A:PHE82 3.9 20.0 1.0 O A:HOH378 4.0 36.9 1.0 O A:VAL97 4.2 17.5 1.0 CE1 A:PHE82 4.3 20.6 1.0 CB A:GLU84 4.4 26.8 0.8 CB A:GLU84 4.4 28.1 0.2 CG A:GLU84 4.4 24.4 0.2 CA A:PRO83 4.5 20.7 0.2 CA A:PRO83 4.6 14.9 0.8 C A:PRO83 4.7 15.2 0.8 C A:PRO83 4.7 20.6 0.2 CA A:GLU84 4.7 22.4 0.8 CA A:GLU84 4.7 23.9 0.2

Chlorine binding site 3 out of 3 in the Human Apo Pd-1 Triple Mutant


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Apo Pd-1 Triple Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:29.0 occ:0.57 CL A:CL202 0.0 29.0 0.6 CL A:CL202 2.7 31.8 0.4 N A:GLU84 3.2 19.0 1.0 O A:HOH327 3.4 32.5 1.0 CB A:PRO83 3.4 21.6 0.2 CG A:GLU84 3.5 24.4 0.2 CA A:PRO83 3.6 20.7 0.2 CA A:PRO83 3.6 14.9 0.8 CB A:PRO83 3.6 17.5 0.8 C A:PRO83 3.9 20.6 0.2 C A:PRO83 3.9 15.2 0.8 CB A:GLU84 4.1 26.8 0.8 CB A:GLU84 4.1 28.1 0.2 CA A:GLU84 4.2 22.4 0.8 CA A:GLU84 4.3 23.9 0.2 CE1 A:PHE82 4.4 20.6 1.0 CD1 A:PHE82 4.5 20.0 1.0 O A:HOH329 4.7 22.8 1.0 O A:HOH387 4.7 20.7 0.6 O A:GLU84 4.8 23.6 1.0 CG A:PRO83 4.8 19.0 0.8 CG A:PRO83 4.9 19.4 0.2

S.Tang, P.S.Kim. A High-Affinity Human Pd-1/Pd-L2 Complex Informs Avenues For Small-Molecule Immune Checkpoint Drug Discovery. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31727844
DOI: 10.1073/PNAS.1916916116