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

Protein crystallography data

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

Chlorine Binding Sites:

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 6v7y

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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 6v7y

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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 6v7y

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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 6v7y

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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 6v7y

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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

Reference:

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
Page generated: Sat Dec 12 14:15:30 2020

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