Chlorine in PDB 6umv: Human Apo Pd-1 Double Mutant

The structure of Human Apo Pd-1 Double Mutant, PDB code: 6umv 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)	36.52 / 1.42
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	46.199, 46.199, 89.407, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 18.9

The binding sites of Chlorine atom in the Human Apo Pd-1 Double Mutant (pdb code 6umv). 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 Double Mutant, PDB code: 6umv:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Human Apo Pd-1 Double 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 Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:22.8 occ:0.00 N A:LEU138 3.3 18.3 1.0 N A:PHE37 3.3 19.4 1.0 CB A:LEU138 3.5 19.6 1.0 CA A:THR36 3.5 21.3 1.0 O A:HOH331 3.6 34.5 1.0 CG A:LEU138 3.8 20.2 1.0 CB A:SER137 3.9 16.9 1.0 CA A:LEU138 3.9 18.0 1.0 C A:THR36 3.9 19.8 1.0 CB A:THR36 3.9 25.1 1.0 O A:PHE37 4.1 22.8 1.0 O A:PRO35 4.2 20.7 1.0 C A:SER137 4.2 16.9 1.0 CA A:SER137 4.2 17.5 1.0 O A:LEU138 4.2 19.1 1.0 O A:HOH336 4.2 47.9 1.0 CA A:PHE37 4.3 18.0 1.0 CG2 A:THR36 4.4 25.1 1.0 CD1 A:LEU138 4.4 26.1 1.0 CB A:PHE37 4.4 18.9 1.0 C A:LEU138 4.5 19.2 1.0 C A:PHE37 4.6 20.1 1.0 N A:THR36 4.7 19.8 1.0 OG A:SER137 4.7 17.6 1.0 C A:PRO35 4.9 19.2 1.0

Chlorine binding site 2 out of 3 in the Human Apo Pd-1 Double 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 Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:43.0 occ:0.41 CL A:CL202 0.0 43.0 0.4 CL A:CL202 2.6 36.1 0.6 O A:HOH318 2.6 28.3 1.0 O A:HOH359 2.9 33.7 1.0 N A:GLU84 3.7 25.5 1.0 CD1 A:PHE82 3.9 30.4 1.0 O A:VAL97 4.2 23.9 1.0 CB A:GLU84 4.2 31.9 0.4 CB A:GLU84 4.2 34.8 0.6 CG A:GLU84 4.3 32.7 0.4 CE1 A:PHE82 4.3 30.1 1.0 CA A:PRO83 4.4 21.8 0.3 CA A:GLU84 4.5 29.2 0.4 C A:PRO83 4.5 24.0 0.3 CA A:GLU84 4.5 29.8 0.6 CA A:PRO83 4.5 20.9 0.7 C A:PRO83 4.5 21.2 0.7 CG A:PHE82 4.9 26.3 1.0

Chlorine binding site 3 out of 3 in the Human Apo Pd-1 Double 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 Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:36.1 occ:0.59 CL A:CL202 0.0 36.1 0.6 CL A:CL202 2.6 43.0 0.4 N A:GLU84 3.1 25.5 1.0 CG A:GLU84 3.3 32.7 0.4 O A:HOH343 3.3 42.5 1.0 CB A:PRO83 3.4 21.5 0.3 CA A:PRO83 3.5 21.8 0.3 CA A:PRO83 3.6 20.9 0.7 CB A:PRO83 3.6 24.7 0.7 C A:PRO83 3.8 24.0 0.3 C A:PRO83 3.8 21.2 0.7 CB A:GLU84 4.0 31.9 0.4 CB A:GLU84 4.1 34.8 0.6 CA A:GLU84 4.2 29.2 0.4 CA A:GLU84 4.2 29.8 0.6 CE1 A:PHE82 4.3 30.1 1.0 CD1 A:PHE82 4.4 30.4 1.0 O A:HOH318 4.6 28.3 1.0 O A:GLU84 4.7 31.2 1.0 O A:HOH359 4.7 33.7 1.0 CG A:PRO83 4.8 20.9 0.3 CG A:PRO83 4.8 25.5 0.7 N A:PRO83 5.0 21.3 0.3 N A:PRO83 5.0 20.6 0.7 C A:GLU84 5.0 29.8 1.0

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