Bromine in PDB 5itf: Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant
Protein crystallography data
The structure of Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant, PDB code: 5itf
was solved by
K.P.Bzymek,
J.C.Williams,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.14 /
2.51
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.010,
82.210,
211.900,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.4 /
22.3
|
Bromine Binding Sites:
The binding sites of Bromine atom in the Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant
(pdb code 5itf). This binding sites where shown within
5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the
Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant, PDB code: 5itf:
Jump to Bromine binding site number:
1;
2;
3;
Bromine binding site 1 out
of 3 in 5itf
Go back to
Bromine Binding Sites List in 5itf
Bromine binding site 1 out
of 3 in the Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 1 of Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Br3
b:56.2
occ:0.43
|
BR
|
E:6DU3
|
0.0
|
56.2
|
0.4
|
CD2
|
E:6DU3
|
1.0
|
52.7
|
0.6
|
CE2
|
E:6DU3
|
1.8
|
52.8
|
0.6
|
CD1
|
E:6DU3
|
2.0
|
52.8
|
0.4
|
CG
|
E:6DU3
|
2.2
|
51.1
|
0.6
|
CG
|
E:6DU3
|
2.9
|
51.0
|
0.4
|
CB
|
E:6DU3
|
2.9
|
46.7
|
0.6
|
CE1
|
E:6DU3
|
3.0
|
53.0
|
0.4
|
CZ
|
E:6DU3
|
3.1
|
53.2
|
0.6
|
CB
|
E:6DU3
|
3.1
|
47.3
|
0.4
|
OH
|
A:TYR87
|
3.2
|
40.2
|
1.0
|
CD1
|
E:6DU3
|
3.3
|
52.5
|
0.6
|
CA
|
E:6DU3
|
3.4
|
43.6
|
0.6
|
CA
|
E:6DU3
|
3.4
|
43.9
|
0.4
|
C
|
E:ARG9
|
3.5
|
28.3
|
1.0
|
O
|
E:ARG9
|
3.6
|
30.1
|
1.0
|
O
|
A:HOH440
|
3.6
|
30.3
|
1.0
|
CD2
|
E:LEU10
|
3.6
|
42.7
|
1.0
|
CE1
|
E:6DU3
|
3.7
|
53.6
|
0.6
|
N
|
E:LEU10
|
3.7
|
36.0
|
1.0
|
NE2
|
B:GLN39
|
3.8
|
46.1
|
1.0
|
N
|
E:ARG9
|
3.9
|
41.7
|
1.0
|
CG
|
E:LEU10
|
4.0
|
34.8
|
1.0
|
CA
|
E:ARG9
|
4.0
|
31.4
|
1.0
|
C
|
E:ARG8
|
4.0
|
54.6
|
1.0
|
O
|
E:ARG8
|
4.0
|
62.9
|
1.0
|
CA
|
E:LEU10
|
4.1
|
33.0
|
1.0
|
CD2
|
E:6DU3
|
4.2
|
52.9
|
0.4
|
N
|
E:ASP4
|
4.2
|
38.6
|
1.0
|
CZ
|
E:6DU3
|
4.2
|
53.9
|
0.4
|
C
|
E:6DU3
|
4.2
|
41.4
|
0.6
|
C
|
E:6DU3
|
4.3
|
41.7
|
0.4
|
CD
|
B:GLN39
|
4.3
|
41.2
|
1.0
|
OD2
|
A:ASP85
|
4.4
|
45.5
|
1.0
|
OE1
|
A:GLN38
|
4.4
|
44.2
|
1.0
|
CZ
|
A:TYR87
|
4.5
|
35.3
|
1.0
|
N
|
E:6DU3
|
4.5
|
48.7
|
0.6
|
N
|
E:6DU3
|
4.5
|
48.7
|
0.4
|
CB
|
E:LEU10
|
4.6
|
29.7
|
1.0
|
CE2
|
E:6DU3
|
4.7
|
54.0
|
0.4
|
CA
|
E:ARG8
|
4.7
|
54.2
|
1.0
|
CG
|
B:GLN39
|
4.8
|
30.2
|
1.0
|
OE1
|
B:GLN39
|
4.9
|
41.9
|
1.0
|
|
Bromine binding site 2 out
of 3 in 5itf
Go back to
Bromine Binding Sites List in 5itf
Bromine binding site 2 out
of 3 in the Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 2 of Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Br3
b:56.0
occ:0.57
|
BR
|
E:6DU3
|
0.0
|
56.0
|
0.6
|
CD2
|
E:6DU3
|
0.9
|
52.9
|
0.4
|
CE2
|
E:6DU3
|
1.7
|
54.0
|
0.4
|
CD1
|
E:6DU3
|
2.0
|
52.5
|
0.6
|
CG
|
E:6DU3
|
2.2
|
51.0
|
0.4
|
CE1
|
E:6DU3
|
2.9
|
53.6
|
0.6
|
CG
|
E:6DU3
|
2.9
|
51.1
|
0.6
|
CZ
|
E:6DU3
|
2.9
|
53.9
|
0.4
|
CB
|
E:6DU3
|
3.0
|
47.3
|
0.4
|
CB
|
E:6DU3
|
3.1
|
46.7
|
0.6
|
O
|
E:6DU3
|
3.2
|
45.0
|
0.6
|
CD1
|
E:6DU3
|
3.3
|
52.8
|
0.4
|
O
|
E:6DU3
|
3.3
|
45.0
|
0.4
|
O
|
B:GLN39
|
3.4
|
36.6
|
1.0
|
C
|
B:SER40
|
3.4
|
35.6
|
1.0
|
N
|
B:PRO41
|
3.5
|
35.1
|
1.0
|
C
|
E:6DU3
|
3.5
|
41.4
|
0.6
|
CE1
|
E:6DU3
|
3.5
|
53.0
|
0.4
|
C
|
E:6DU3
|
3.5
|
41.7
|
0.4
|
CD2
|
E:LEU5
|
3.7
|
43.6
|
1.0
|
CD
|
B:PRO41
|
3.7
|
31.1
|
1.0
|
CA
|
B:SER40
|
3.8
|
35.1
|
1.0
|
O
|
B:SER40
|
3.8
|
39.7
|
1.0
|
CG
|
E:LEU5
|
3.8
|
43.4
|
1.0
|
C
|
B:GLN39
|
3.9
|
34.7
|
1.0
|
CA
|
E:6DU3
|
3.9
|
43.9
|
0.4
|
CA
|
E:6DU3
|
4.0
|
43.6
|
0.6
|
CA
|
B:PRO41
|
4.0
|
34.4
|
1.0
|
CG
|
B:PRO41
|
4.0
|
31.6
|
1.0
|
N
|
B:SER40
|
4.0
|
33.0
|
1.0
|
N
|
E:LEU5
|
4.0
|
36.9
|
1.0
|
N
|
E:ASP4
|
4.1
|
38.6
|
1.0
|
C
|
E:ASP4
|
4.1
|
34.3
|
1.0
|
CZ
|
E:6DU3
|
4.2
|
53.2
|
0.6
|
CD2
|
E:6DU3
|
4.2
|
52.7
|
0.6
|
CA
|
E:LEU5
|
4.3
|
48.7
|
1.0
|
O
|
E:ASP4
|
4.5
|
35.2
|
1.0
|
CA
|
E:ASP4
|
4.5
|
39.9
|
1.0
|
CB
|
B:PRO41
|
4.6
|
32.1
|
1.0
|
CG
|
B:GLN39
|
4.7
|
30.2
|
1.0
|
CB
|
E:LEU5
|
4.7
|
42.0
|
1.0
|
CE2
|
E:6DU3
|
4.7
|
52.8
|
0.6
|
CB
|
B:GLN39
|
4.9
|
25.8
|
1.0
|
N
|
E:6DU3
|
4.9
|
48.7
|
0.4
|
N
|
E:6DU3
|
4.9
|
48.7
|
0.6
|
CD1
|
E:LEU5
|
5.0
|
47.9
|
1.0
|
CA
|
B:GLN39
|
5.0
|
31.6
|
1.0
|
|
Bromine binding site 3 out
of 3 in 5itf
Go back to
Bromine Binding Sites List in 5itf
Bromine binding site 3 out
of 3 in the Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant
Mono view
Stereo pair view
|
A full contact list of Bromine with other atoms in the Br binding
site number 3 of Cetuximab Fab in Complex with 2-Bromophenylalanine Meditope Variant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Br3
b:66.2
occ:1.00
|
BR
|
F:6DU3
|
0.0
|
66.2
|
1.0
|
CD1
|
F:6DU3
|
2.0
|
55.9
|
1.0
|
CG
|
F:6DU3
|
2.9
|
50.2
|
1.0
|
CE1
|
F:6DU3
|
3.0
|
53.1
|
1.0
|
CB
|
F:6DU3
|
3.1
|
48.7
|
1.0
|
O
|
D:GLN39
|
3.5
|
39.1
|
1.0
|
C
|
F:6DU3
|
3.6
|
38.1
|
1.0
|
O
|
F:6DU3
|
3.7
|
37.9
|
1.0
|
N
|
F:ASP4
|
3.9
|
38.0
|
1.0
|
C
|
D:SER40
|
3.9
|
37.9
|
1.0
|
C
|
F:ASP4
|
3.9
|
37.5
|
1.0
|
N
|
D:PRO41
|
4.0
|
36.4
|
1.0
|
CA
|
F:6DU3
|
4.0
|
38.9
|
1.0
|
C
|
D:GLN39
|
4.0
|
36.5
|
1.0
|
CD2
|
F:LEU5
|
4.0
|
45.9
|
1.0
|
O
|
F:ASP4
|
4.0
|
37.6
|
1.0
|
N
|
F:LEU5
|
4.1
|
51.4
|
1.0
|
CG
|
F:LEU5
|
4.1
|
45.2
|
1.0
|
CD
|
D:PRO41
|
4.1
|
25.3
|
1.0
|
CA
|
D:SER40
|
4.1
|
34.8
|
1.0
|
O
|
D:SER40
|
4.2
|
41.7
|
1.0
|
N
|
D:SER40
|
4.2
|
35.8
|
1.0
|
CD2
|
F:6DU3
|
4.2
|
42.5
|
1.0
|
CZ
|
F:6DU3
|
4.2
|
56.2
|
1.0
|
CG
|
D:GLN39
|
4.3
|
30.1
|
1.0
|
CA
|
F:LEU5
|
4.3
|
51.0
|
1.0
|
CA
|
F:ASP4
|
4.4
|
38.1
|
1.0
|
CG
|
D:PRO41
|
4.4
|
25.8
|
1.0
|
CA
|
D:PRO41
|
4.5
|
37.5
|
1.0
|
CB
|
D:GLN39
|
4.7
|
32.1
|
1.0
|
CE2
|
F:6DU3
|
4.8
|
52.3
|
1.0
|
CB
|
F:LEU5
|
4.8
|
46.8
|
1.0
|
CA
|
D:GLN39
|
5.0
|
36.7
|
1.0
|
|
Reference:
K.P.Bzymek,
K.A.Avery,
Y.Ma,
D.A.Horne,
J.C.Williams.
Natural and Non-Natural Amino-Acid Side-Chain Substitutions: Affinity and Diffraction Studies of Meditope-Fab Complexes. Acta Crystallogr F Struct V. 72 820 2016BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 27834791
DOI: 10.1107/S2053230X16016149
Page generated: Thu Jul 11 00:05:19 2024
|