Chlorine in PDB 6v7y: Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5

The structure of Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5, PDB code: 6v7y was solved by A.Shahine, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.73 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	73.270, 73.270, 261.077, 90.00, 90.00, 120.00
R / Rfree (%)	24.1 / 27.6

The binding sites of Chlorine atom in the Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5 (pdb code 6v7y). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5, PDB code: 6v7y:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:72.8 occ:1.00 NE2 A:HIS112 3.6 45.8 1.0 CE1 A:HIS112 3.8 46.0 1.0 NE2 A:GLN124 4.4 56.1 1.0 OE1 A:GLN124 4.8 69.9 1.0 CB A:PHE110 4.8 34.8 1.0 CD2 A:HIS112 4.9 45.2 1.0

Chlorine binding site 2 out of 5 in the Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:69.3 occ:1.00 N A:GLY104 3.5 69.4 1.0 C8 A:NAG401 3.6 99.1 1.0 CA A:PRO103 4.1 64.9 1.0 C7 A:NAG401 4.2 98.5 1.0 N2 A:NAG401 4.2 96.1 1.0 C A:PRO103 4.3 70.4 1.0 CA A:GLY104 4.4 71.2 1.0 N A:ASN105 4.5 69.5 1.0 CB A:PRO103 4.6 68.5 1.0 NE2 A:GLN2 4.7 46.7 1.0 C A:GLY104 4.9 74.6 1.0

Chlorine binding site 3 out of 5 in the Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:86.7 occ:1.00 N A:SER193 3.2 97.6 1.0 CB A:PRO192 3.5 0.6 1.0 CA A:PRO192 3.5 98.2 1.0 C A:PRO192 3.8 0.4 1.0 C A:SER193 3.9 0.6 1.0 CA A:SER193 4.1 0.5 1.0 O A:SER193 4.3 63.2 1.0 CG A:PRO192 4.6 0.2 1.0 O A:HOH565 4.8 57.5 1.0 O A:HOH503 4.8 50.9 1.0 O A:PRO192 4.8 97.8 1.0 N A:PRO192 4.9 96.2 1.0

Chlorine binding site 4 out of 5 in the Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:30.0 occ:1.00 N A:ASP42 3.2 54.4 1.0 OD2 A:ASP42 3.7 30.0 1.0 OG A:SER41 3.7 65.3 1.0 CG A:ASP42 3.7 30.0 1.0 CA A:SER41 4.0 55.1 1.0 CB A:ASP42 4.1 30.0 1.0 C A:SER41 4.1 58.0 1.0 CA A:ASP42 4.1 54.9 1.0 OD1 A:ASP42 4.2 30.0 1.0 CB A:SER41 4.3 57.9 1.0 N A:THR43 4.3 56.0 1.0 CG2 A:THR43 4.6 61.0 1.0 C A:ASP42 4.7 58.6 1.0

Chlorine binding site 5 out of 5 in the Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human CD1D Presenting Alpha-Galactosylceramide in Complex with Vhh Nanobody 1D5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl105 b:76.7 occ:1.00 O B:HOH222 3.4 62.2 1.0 O B:HOH217 3.5 61.5 1.0 NH2 B:ARG45 3.8 69.4 1.0 CD B:ARG45 4.1 61.0 1.0 NH2 B:ARG81 4.2 60.1 1.0 CB B:ARG45 4.4 58.0 1.0 CZ B:ARG45 4.7 83.8 1.0 NH1 B:ARG81 4.8 62.9 1.0 NE B:ARG45 4.8 68.3 1.0 CG B:ARG45 4.9 60.9 1.0 CZ B:ARG81 5.0 73.1 1.0

A.Shahine, J.Rossjohn. A Single-Domain Bispecific Antibody Targeting CD1D and the Nkt T-Cell Receptor Induces A Potent Antitumor Response. Nat Cancer 2020.
ISSN: ESSN 2662-1347
DOI: 10.1038/S43018-020-00111-6