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.
Protein crystallography data
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
|
Fluorine Binding Sites:
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 4nhc
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Fluorine Binding Sites List in 4nhc
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 4nhc
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Fluorine Binding Sites List in 4nhc
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 4nhc
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Fluorine Binding Sites List in 4nhc
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 4nhc
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Fluorine Binding Sites List in 4nhc
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 4nhc
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Fluorine Binding Sites List in 4nhc
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 4nhc
Go back to
Fluorine Binding Sites List in 4nhc
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
|
|
Reference:
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
Page generated: Thu Aug 1 04:16:17 2024
|