Fluorine in PDB 4nhc: Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41.

The structure of Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41., PDB code: 4nhc was solved by A.Irimia, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.95 / 2.91
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	226.107, 226.107, 41.824, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 26.8

The binding sites of Fluorine atom in the Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41. (pdb code 4nhc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41., PDB code: 4nhc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41. within 5.0Å range: probe atom residue distance (Å) B Occ L:F301 b:0.6 occ:0.80 F1 L:TFA301 0.0 0.6 0.8 C2 L:TFA301 1.3 0.7 0.8 F2 L:TFA301 2.2 0.1 0.8 F3 L:TFA301 2.2 0.8 0.8 C1 L:TFA301 2.3 0.7 0.8 O L:TFA301 2.6 0.3 0.8 CB H:SER134 2.7 73.7 1.0 CE1 L:PHE116 3.3 63.2 1.0 OXT L:TFA301 3.5 0.6 0.8 OG H:SER134 3.6 74.2 1.0 CD1 L:PHE116 3.7 64.4 1.0 O H:THR133 3.7 71.5 1.0 C H:THR133 3.8 69.9 1.0 CA H:SER134 3.8 73.4 1.0 N H:SER134 3.8 70.0 1.0 CZ L:PHE116 4.1 58.3 1.0 O L:VAL115 4.1 61.9 1.0 N H:THR133 4.6 65.7 1.0 CA H:THR133 4.7 67.7 1.0 CG L:PHE116 4.7 61.9 1.0 CE L:LYS207 4.7 72.4 1.0 C H:SER130 4.8 66.8 1.0 C H:SER134 5.0 74.0 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41. within 5.0Å range: probe atom residue distance (Å) B Occ L:F301 b:0.1 occ:0.80 F2 L:TFA301 0.0 0.1 0.8 C2 L:TFA301 1.3 0.7 0.8 F1 L:TFA301 2.2 0.6 0.8 F3 L:TFA301 2.2 0.8 0.8 C1 L:TFA301 2.3 0.7 0.8 O L:VAL115 2.7 61.9 1.0 CE L:LYS207 2.8 72.4 1.0 OXT L:TFA301 2.8 0.6 0.8 O L:TFA301 3.3 0.3 0.8 CD L:LYS207 3.6 71.4 1.0 NZ L:LYS207 3.8 68.5 1.0 C L:VAL115 3.8 57.1 1.0 O H:LYS129 4.0 65.9 1.0 CD1 L:PHE116 4.1 64.4 1.0 CG L:LYS207 4.1 68.6 1.0 CA L:PHE116 4.3 64.3 1.0 CE1 L:PHE116 4.4 63.2 1.0 N L:PHE116 4.5 60.7 1.0 CB H:SER134 4.6 73.7 1.0 O H:THR133 4.7 71.5 1.0 CG L:PHE116 4.7 61.9 1.0 C H:LYS129 4.7 70.2 1.0 CA L:VAL115 4.9 55.7 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41. within 5.0Å range: probe atom residue distance (Å) B Occ L:F301 b:0.8 occ:0.80 F3 L:TFA301 0.0 0.8 0.8 C2 L:TFA301 1.3 0.7 0.8 F2 L:TFA301 2.2 0.1 0.8 F1 L:TFA301 2.2 0.6 0.8 C1 L:TFA301 2.3 0.7 0.8 OXT L:TFA301 2.8 0.6 0.8 O L:TFA301 3.3 0.3 0.8 CE L:LYS207 3.4 72.4 1.0 CB H:SER134 3.4 73.7 1.0 OG H:SER134 3.7 74.2 1.0 NZ L:LYS207 4.1 68.5 1.0 O H:THR133 4.2 71.5 1.0 O L:VAL115 4.5 61.9 1.0 CA H:SER134 4.6 73.4 1.0 CD L:LYS207 4.6 71.4 1.0 C H:THR133 4.8 69.9 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41. within 5.0Å range: probe atom residue distance (Å) B Occ H:F302 b:0.6 occ:0.92 F1 H:TFA302 0.0 0.6 0.9 C2 H:TFA302 1.3 0.5 0.9 F2 H:TFA302 2.2 0.1 0.9 F3 H:TFA302 2.2 0.1 0.9 C1 H:TFA302 2.3 0.8 0.9 O H:TFA302 2.6 0.5 0.9 OXT H:TFA302 3.4 1.0 0.9 OE1 H:GLN39 3.6 64.8 1.0 CD H:GLN39 3.8 65.0 1.0 O H:GLN39 3.9 59.8 1.0 CG2 H:VAL89 3.9 38.6 1.0 CG H:GLN39 4.1 61.7 1.0 CB H:VAL89 4.2 37.1 1.0 NE2 H:GLN39 4.4 66.6 1.0 O H:ALA40 4.4 58.4 1.0 CB H:GLN39 4.4 57.6 1.0 C H:GLN39 4.7 60.0 1.0 C H:ALA40 5.0 61.3 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41. within 5.0Å range: probe atom residue distance (Å) B Occ H:F302 b:0.1 occ:0.92 F2 H:TFA302 0.0 0.1 0.9 C2 H:TFA302 1.3 0.5 0.9 F3 H:TFA302 2.2 0.1 0.9 F1 H:TFA302 2.2 0.6 0.9 C1 H:TFA302 2.3 0.8 0.9 O H:TFA302 3.0 0.5 0.9 CA H:PRO41 3.1 66.2 1.0 OXT H:TFA302 3.1 1.0 0.9 O H:ALA40 3.2 58.4 1.0 N H:PRO41 3.4 66.1 1.0 C H:ALA40 3.4 61.3 1.0 O H:GLN39 3.6 59.8 1.0 N H:GLY42 3.7 75.6 1.0 C H:PRO41 3.9 71.9 1.0 CB H:PRO41 4.1 62.1 1.0 CD H:PRO41 4.4 64.2 1.0 C H:GLN39 4.4 60.0 1.0 CG H:PRO41 4.4 64.0 1.0 CA H:ALA40 4.5 60.6 1.0 CG2 H:VAL89 4.6 38.6 1.0 N H:ALA40 4.8 60.4 1.0 CG H:GLN39 4.9 61.7 1.0 N H:VAL89 5.0 51.4 1.0 CA H:GLY42 5.0 75.2 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Hiv-1 Neutralizing Antibody 4E10 Fab Fragment in Complex with A Hydrocarbon-Stapled Peptide Containing the 4E10 Epitope on GP41. within 5.0Å range: probe atom residue distance (Å) B Occ H:F302 b:0.1 occ:0.92 F3 H:TFA302 0.0 0.1 0.9 C2 H:TFA302 1.3 0.5 0.9 F2 H:TFA302 2.2 0.1 0.9 F1 H:TFA302 2.2 0.6 0.9 C1 H:TFA302 2.3 0.8 0.9 OXT H:TFA302 2.6 1.0 0.9 O H:TFA302 3.4 0.5 0.9 CG2 H:VAL89 4.7 38.6 1.0 CA H:PRO41 4.7 66.2 1.0 N H:GLY42 4.8 75.6 1.0

G.H.Bird, A.Irimia, G.Ofek, P.D.Kwong, I.A.Wilson, L.D.Walensky. Stapled Hiv-1 Peptides Recapitulate Antigenic Structures and Engage Broadly Neutralizing Antibodies. Nat.Struct.Mol.Biol. 2014.
ISSN: ESSN 1545-9985
PubMed: 25420104
DOI: 10.1038/NSMB.2922