Fluorine in PDB 3d3v: The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide

The structure of The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide, PDB code: 3d3v was solved by O.Y.Borbulevych, J.R.Clemens, B.M.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	224.450, 48.537, 93.794, 90.00, 90.61, 90.00
R / Rfree (%)	22 / 27.8

The binding sites of Fluorine atom in the The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide (pdb code 3d3v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide, PDB code: 3d3v:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:F5 b:66.2 occ:0.50 F2 C:F2F5 0.0 66.2 0.5 CZ C:F2F5 0.9 66.7 0.5 F1 C:F2F5 1.1 66.8 0.5 CE2 C:F2F5 1.3 66.1 0.5 CE1 C:F2F5 1.6 66.7 0.5 CE2 C:F2F5 2.0 66.7 0.5 CZ C:F2F5 2.3 66.1 0.5 CD2 C:F2F5 2.4 66.3 0.5 F1 C:F2F5 2.6 66.2 0.5 F2 C:F2F5 2.8 66.8 0.5 CD1 C:F2F5 2.8 67.0 0.5 CD2 C:F2F5 3.1 66.6 0.5 C D:ASP99 3.2 57.9 1.0 CA D:ASP99 3.4 56.3 1.0 CG C:F2F5 3.4 66.6 0.5 N D:SER100 3.5 59.4 1.0 O D:ASP99 3.5 57.6 1.0 CE1 C:F2F5 3.6 66.0 0.5 CG C:F2F5 3.6 65.8 0.5 N D:ASP99 3.7 53.9 1.0 NH2 E:ARG95 4.0 51.2 1.0 CG2 D:THR93 4.1 58.3 1.0 CD1 C:F2F5 4.1 65.9 0.5 CB E:PRO103 4.1 52.5 1.0 CA D:SER100 4.1 59.1 1.0 O E:HOH249 4.2 30.0 1.0 OG1 D:THR93 4.3 56.3 1.0 OG D:SER31 4.3 67.6 1.0 O C:GLY4 4.3 64.3 1.0 CG E:PRO103 4.4 53.5 1.0 C D:THR98 4.4 53.3 1.0 O D:THR98 4.8 53.3 1.0 C C:GLY4 4.8 64.0 1.0 CB D:SER31 4.8 66.2 1.0 CB D:ASP99 4.8 57.4 1.0 CB D:THR93 4.8 56.9 1.0 CB C:F2F5 4.9 65.8 0.5 CB C:F2F5 4.9 66.3 0.5 CA E:PRO103 4.9 51.8 1.0 O E:HOH253 4.9 31.5 1.0

Fluorine binding site 2 out of 4 in the The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:F5 b:66.8 occ:0.50 F2 C:F2F5 0.0 66.8 0.5 CZ C:F2F5 0.7 66.1 0.5 F1 C:F2F5 0.9 66.2 0.5 CE2 C:F2F5 1.3 66.7 0.5 CE1 C:F2F5 1.5 66.0 0.5 CE2 C:F2F5 2.0 66.1 0.5 CZ C:F2F5 2.3 66.7 0.5 CD2 C:F2F5 2.3 66.6 0.5 F1 C:F2F5 2.7 66.8 0.5 CD1 C:F2F5 2.8 65.9 0.5 F2 C:F2F5 2.8 66.2 0.5 CD2 C:F2F5 3.1 66.3 0.5 OG D:SER31 3.2 67.6 1.0 CB D:GLN30 3.3 66.7 1.0 CG C:F2F5 3.4 65.8 0.5 CG C:F2F5 3.6 66.6 0.5 CE1 C:F2F5 3.6 66.7 0.5 C D:GLN30 3.8 66.2 1.0 N D:SER31 3.8 65.8 1.0 CA D:GLN30 4.1 66.6 1.0 CD1 C:F2F5 4.1 67.0 0.5 CB D:SER31 4.1 66.2 1.0 O D:GLN30 4.1 66.3 1.0 O D:THR98 4.4 53.3 1.0 CA C:GLY4 4.5 63.1 1.0 CG D:GLN30 4.5 67.3 1.0 CA D:SER31 4.5 66.1 1.0 OE1 D:GLN30 4.5 69.5 1.0 CD D:GLN30 4.6 68.2 1.0 CA D:ASP99 4.6 56.3 1.0 C D:THR98 4.6 53.3 1.0 N D:ASP99 4.6 53.9 1.0 CG E:PRO103 4.7 53.5 1.0 C C:GLY4 4.7 64.0 1.0 CB C:F2F5 4.8 66.3 0.5 CB C:F2F5 4.9 65.8 0.5 N D:GLN30 4.9 66.1 1.0

Fluorine binding site 3 out of 4 in the The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:F5 b:66.2 occ:0.50 F1 C:F2F5 0.0 66.2 0.5 F2 C:F2F5 0.9 66.8 0.5 CZ C:F2F5 1.3 66.1 0.5 CE2 C:F2F5 1.9 66.7 0.5 F1 C:F2F5 2.2 66.8 0.5 CE2 C:F2F5 2.3 66.1 0.5 CZ C:F2F5 2.3 66.7 0.5 CE1 C:F2F5 2.4 66.0 0.5 F2 C:F2F5 2.6 66.2 0.5 OG D:SER31 2.7 67.6 1.0 N D:SER31 3.0 65.8 1.0 CD2 C:F2F5 3.1 66.6 0.5 CB D:GLN30 3.3 66.7 1.0 C D:GLN30 3.3 66.2 1.0 CB D:SER31 3.4 66.2 1.0 CD2 C:F2F5 3.6 66.3 0.5 CD1 C:F2F5 3.6 65.9 0.5 CE1 C:F2F5 3.7 66.7 0.5 CA D:GLN30 3.8 66.6 1.0 CA D:SER31 3.8 66.1 1.0 O D:GLN30 3.8 66.3 1.0 CG C:F2F5 4.1 65.8 0.5 CG C:F2F5 4.2 66.6 0.5 O D:THR98 4.3 53.3 1.0 CG2 D:THR93 4.3 58.3 1.0 C D:THR98 4.4 53.3 1.0 N D:ASP99 4.4 53.9 1.0 N D:GLN30 4.4 66.1 1.0 O D:THR93 4.5 56.2 1.0 CD1 C:F2F5 4.5 67.0 0.5 CA D:ASP99 4.6 56.3 1.0 CG D:GLN30 4.7 67.3 1.0 CG E:PRO103 4.7 53.5 1.0 CB E:PRO103 4.8 52.5 1.0 C D:THR93 4.9 55.3 1.0 CD D:GLN30 4.9 68.2 1.0

Fluorine binding site 4 out of 4 in the The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Complex Between Tcr A6 and Human Class I Mhc Hla-A2 with the Modified Htlv-1 Tax (Y5(3,4-Difluorophenylalanine)) Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:F5 b:66.8 occ:0.50 F1 C:F2F5 0.0 66.8 0.5 F2 C:F2F5 1.1 66.2 0.5 CZ C:F2F5 1.3 66.7 0.5 CE2 C:F2F5 1.9 66.1 0.5 F1 C:F2F5 2.2 66.2 0.5 CE2 C:F2F5 2.3 66.7 0.5 CZ C:F2F5 2.4 66.1 0.5 CE1 C:F2F5 2.4 66.7 0.5 F2 C:F2F5 2.7 66.8 0.5 CD2 C:F2F5 3.1 66.3 0.5 CG2 D:THR93 3.2 58.3 1.0 OG D:SER31 3.5 67.6 1.0 CD2 C:F2F5 3.6 66.6 0.5 CD1 C:F2F5 3.6 67.0 0.5 CB E:PRO103 3.7 52.5 1.0 CE1 C:F2F5 3.7 66.0 0.5 CB D:SER31 3.8 66.2 1.0 C D:ASP99 3.9 57.9 1.0 OG1 D:THR93 4.0 56.3 1.0 N D:ASP99 4.0 53.9 1.0 CA D:ASP99 4.0 56.3 1.0 NH2 E:ARG95 4.0 51.2 1.0 O D:ASP99 4.1 57.6 1.0 CG C:F2F5 4.1 66.6 0.5 CG E:PRO103 4.1 53.5 1.0 CB D:THR93 4.2 56.9 1.0 CG C:F2F5 4.3 65.8 0.5 N D:SER31 4.3 65.8 1.0 N D:SER100 4.4 59.4 1.0 O E:HOH249 4.5 30.0 1.0 CD1 C:F2F5 4.5 65.9 0.5 C D:THR98 4.5 53.3 1.0 CA E:PRO103 4.6 51.8 1.0 CA D:SER31 4.7 66.1 1.0 C D:THR93 4.7 55.3 1.0 O D:THR93 4.8 56.2 1.0 N D:THR98 4.9 54.2 1.0 O D:THR98 5.0 53.3 1.0

K.H.Piepenbrink, O.Y.Borbulevych, R.F.Sommese, J.Clemens, K.M.Armstrong, C.Desmond, P.Do, B.M.Baker. Fluorine Substitutions in An Antigenic Peptide Selectively Modulate T-Cell Receptor Binding in A Minimally Perturbing Manner. Biochem.J. V. 423 353 2009.
ISSN: ISSN 0264-6021
PubMed: 19698083
DOI: 10.1042/BJ20090732