Iron in PDB 6e40: Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat
Enzymatic activity of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat
All present enzymatic activity of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat:
1.13.11.52;
Protein crystallography data
The structure of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat, PDB code: 6e40
was solved by
S.Luo,
L.Tong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.86 /
2.31
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.367,
200.144,
114.741,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
25.4
|
Other elements in 6e40:
The structure of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat
(pdb code 6e40). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat, PDB code: 6e40:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6e40
Go back to
Iron Binding Sites List in 6e40
Iron binding site 1 out
of 4 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:52.4
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
52.4
|
1.0
|
O12
|
A:BBJ502
|
1.8
|
61.1
|
1.0
|
NA
|
A:HEM501
|
2.0
|
51.1
|
1.0
|
NE2
|
A:HIS346
|
2.0
|
56.0
|
1.0
|
NC
|
A:HEM501
|
2.1
|
56.2
|
1.0
|
ND
|
A:HEM501
|
2.1
|
60.4
|
1.0
|
NB
|
A:HEM501
|
2.1
|
54.7
|
1.0
|
CE1
|
A:HIS346
|
2.7
|
51.8
|
1.0
|
N11
|
A:BBJ502
|
2.7
|
68.4
|
1.0
|
C4A
|
A:HEM501
|
3.0
|
57.6
|
1.0
|
C4C
|
A:HEM501
|
3.0
|
57.8
|
1.0
|
C1A
|
A:HEM501
|
3.0
|
60.4
|
1.0
|
C1D
|
A:HEM501
|
3.0
|
56.1
|
1.0
|
C4D
|
A:HEM501
|
3.1
|
56.5
|
1.0
|
C1B
|
A:HEM501
|
3.1
|
56.3
|
1.0
|
C1C
|
A:HEM501
|
3.1
|
54.3
|
1.0
|
C4B
|
A:HEM501
|
3.2
|
51.8
|
1.0
|
CD2
|
A:HIS346
|
3.2
|
55.1
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
58.5
|
1.0
|
CHB
|
A:HEM501
|
3.4
|
57.0
|
1.0
|
CHA
|
A:HEM501
|
3.4
|
55.1
|
1.0
|
CHC
|
A:HEM501
|
3.5
|
52.1
|
1.0
|
C10
|
A:BBJ502
|
3.6
|
67.3
|
1.0
|
N9
|
A:BBJ502
|
3.9
|
64.5
|
1.0
|
ND1
|
A:HIS346
|
4.0
|
50.5
|
1.0
|
CG
|
A:HIS346
|
4.2
|
54.5
|
1.0
|
C3A
|
A:HEM501
|
4.2
|
60.2
|
1.0
|
C2A
|
A:HEM501
|
4.2
|
60.9
|
1.0
|
C3C
|
A:HEM501
|
4.3
|
55.8
|
1.0
|
C2D
|
A:HEM501
|
4.3
|
54.1
|
1.0
|
C3D
|
A:HEM501
|
4.3
|
53.5
|
1.0
|
C2C
|
A:HEM501
|
4.3
|
53.2
|
1.0
|
C2B
|
A:HEM501
|
4.3
|
57.4
|
1.0
|
C3B
|
A:HEM501
|
4.4
|
55.9
|
1.0
|
CB
|
A:ALA264
|
4.5
|
60.7
|
1.0
|
N
|
A:ALA264
|
4.6
|
68.4
|
1.0
|
C13
|
A:BBJ502
|
4.9
|
68.7
|
1.0
|
CA
|
A:ALA264
|
4.9
|
63.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 6e40
Go back to
Iron Binding Sites List in 6e40
Iron binding site 2 out
of 4 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:51.7
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
51.7
|
1.0
|
O12
|
B:BBJ502
|
1.8
|
57.6
|
1.0
|
NE2
|
B:HIS346
|
2.0
|
51.3
|
1.0
|
NA
|
B:HEM501
|
2.0
|
55.9
|
1.0
|
ND
|
B:HEM501
|
2.0
|
50.5
|
1.0
|
NC
|
B:HEM501
|
2.0
|
50.6
|
1.0
|
NB
|
B:HEM501
|
2.0
|
54.2
|
1.0
|
CE1
|
B:HIS346
|
2.7
|
49.3
|
1.0
|
N11
|
B:BBJ502
|
2.8
|
62.2
|
1.0
|
C4A
|
B:HEM501
|
3.0
|
56.6
|
1.0
|
C4D
|
B:HEM501
|
3.0
|
53.6
|
1.0
|
C1A
|
B:HEM501
|
3.0
|
57.0
|
1.0
|
C1D
|
B:HEM501
|
3.0
|
52.2
|
1.0
|
C1B
|
B:HEM501
|
3.1
|
53.3
|
1.0
|
C1C
|
B:HEM501
|
3.1
|
54.5
|
1.0
|
C4C
|
B:HEM501
|
3.1
|
52.9
|
1.0
|
C4B
|
B:HEM501
|
3.1
|
52.8
|
1.0
|
CD2
|
B:HIS346
|
3.1
|
49.4
|
1.0
|
CHA
|
B:HEM501
|
3.4
|
52.4
|
1.0
|
CHB
|
B:HEM501
|
3.4
|
54.0
|
1.0
|
CHD
|
B:HEM501
|
3.4
|
52.7
|
1.0
|
CHC
|
B:HEM501
|
3.4
|
55.3
|
1.0
|
C10
|
B:BBJ502
|
3.6
|
60.1
|
1.0
|
N9
|
B:BBJ502
|
3.8
|
58.7
|
1.0
|
ND1
|
B:HIS346
|
3.9
|
51.2
|
1.0
|
CG
|
B:HIS346
|
4.1
|
47.2
|
1.0
|
C3A
|
B:HEM501
|
4.2
|
57.0
|
1.0
|
C3D
|
B:HEM501
|
4.2
|
48.7
|
1.0
|
C2A
|
B:HEM501
|
4.2
|
60.1
|
1.0
|
C2D
|
B:HEM501
|
4.2
|
50.3
|
1.0
|
C2B
|
B:HEM501
|
4.3
|
58.5
|
1.0
|
C3B
|
B:HEM501
|
4.3
|
55.7
|
1.0
|
C3C
|
B:HEM501
|
4.3
|
54.0
|
1.0
|
C2C
|
B:HEM501
|
4.3
|
55.7
|
1.0
|
CB
|
B:ALA264
|
4.4
|
55.6
|
1.0
|
N
|
B:ALA264
|
4.9
|
55.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 6e40
Go back to
Iron Binding Sites List in 6e40
Iron binding site 3 out
of 4 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:59.1
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
59.1
|
1.0
|
NA
|
C:HEM501
|
2.0
|
58.2
|
1.0
|
ND
|
C:HEM501
|
2.0
|
66.5
|
1.0
|
NC
|
C:HEM501
|
2.1
|
61.5
|
1.0
|
NE2
|
C:HIS346
|
2.1
|
64.0
|
1.0
|
NB
|
C:HEM501
|
2.2
|
58.8
|
1.0
|
CE1
|
C:HIS346
|
2.9
|
63.6
|
1.0
|
C4A
|
C:HEM501
|
3.0
|
62.7
|
1.0
|
C4C
|
C:HEM501
|
3.0
|
62.3
|
1.0
|
C1D
|
C:HEM501
|
3.0
|
61.5
|
1.0
|
C1A
|
C:HEM501
|
3.0
|
66.3
|
1.0
|
C4D
|
C:HEM501
|
3.1
|
62.3
|
1.0
|
C1C
|
C:HEM501
|
3.1
|
61.7
|
1.0
|
C1B
|
C:HEM501
|
3.1
|
62.8
|
1.0
|
C4B
|
C:HEM501
|
3.2
|
56.1
|
1.0
|
CD2
|
C:HIS346
|
3.3
|
63.6
|
1.0
|
CHD
|
C:HEM501
|
3.4
|
64.1
|
1.0
|
CHB
|
C:HEM501
|
3.4
|
61.6
|
1.0
|
CHA
|
C:HEM501
|
3.4
|
64.5
|
1.0
|
CHC
|
C:HEM501
|
3.5
|
56.6
|
1.0
|
N
|
C:ALA264
|
4.1
|
66.8
|
1.0
|
ND1
|
C:HIS346
|
4.1
|
59.9
|
1.0
|
CB
|
C:ALA264
|
4.2
|
61.2
|
1.0
|
C3A
|
C:HEM501
|
4.2
|
65.4
|
1.0
|
C2A
|
C:HEM501
|
4.2
|
64.5
|
1.0
|
C2D
|
C:HEM501
|
4.3
|
62.4
|
1.0
|
C3C
|
C:HEM501
|
4.3
|
61.7
|
1.0
|
C3D
|
C:HEM501
|
4.3
|
62.7
|
1.0
|
C2C
|
C:HEM501
|
4.3
|
61.6
|
1.0
|
CG
|
C:HIS346
|
4.3
|
62.6
|
1.0
|
C2B
|
C:HEM501
|
4.4
|
65.4
|
1.0
|
C3B
|
C:HEM501
|
4.4
|
61.1
|
1.0
|
CA
|
C:ALA264
|
4.6
|
64.6
|
1.0
|
N
|
C:GLY265
|
4.8
|
66.5
|
1.0
|
C
|
C:ALA264
|
4.9
|
69.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 6e40
Go back to
Iron Binding Sites List in 6e40
Iron binding site 4 out
of 4 in the Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of the Indoleamine 2,3-Dioxygenase 1 (IDO1) in Complexed with Ferric Heme and Epacadostat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:47.8
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
47.8
|
1.0
|
O12
|
D:BBJ502
|
1.8
|
55.8
|
1.0
|
NA
|
D:HEM501
|
2.0
|
49.0
|
1.0
|
NB
|
D:HEM501
|
2.0
|
49.4
|
1.0
|
ND
|
D:HEM501
|
2.0
|
47.6
|
1.0
|
NC
|
D:HEM501
|
2.1
|
48.0
|
1.0
|
NE2
|
D:HIS346
|
2.1
|
49.9
|
1.0
|
N11
|
D:BBJ502
|
2.7
|
56.6
|
1.0
|
CE1
|
D:HIS346
|
2.9
|
47.4
|
1.0
|
C4A
|
D:HEM501
|
3.0
|
52.5
|
1.0
|
C1A
|
D:HEM501
|
3.0
|
51.8
|
1.0
|
C1B
|
D:HEM501
|
3.0
|
50.6
|
1.0
|
C4D
|
D:HEM501
|
3.0
|
48.2
|
1.0
|
C1D
|
D:HEM501
|
3.1
|
50.6
|
1.0
|
C4C
|
D:HEM501
|
3.1
|
47.2
|
1.0
|
C4B
|
D:HEM501
|
3.1
|
51.2
|
1.0
|
C1C
|
D:HEM501
|
3.1
|
49.9
|
1.0
|
CD2
|
D:HIS346
|
3.1
|
50.1
|
1.0
|
CHB
|
D:HEM501
|
3.4
|
51.0
|
1.0
|
CHA
|
D:HEM501
|
3.4
|
49.0
|
1.0
|
CHD
|
D:HEM501
|
3.4
|
50.0
|
1.0
|
CHC
|
D:HEM501
|
3.5
|
50.2
|
1.0
|
C10
|
D:BBJ502
|
3.6
|
53.8
|
1.0
|
N9
|
D:BBJ502
|
4.0
|
52.1
|
1.0
|
ND1
|
D:HIS346
|
4.1
|
48.9
|
1.0
|
CG
|
D:HIS346
|
4.2
|
49.5
|
1.0
|
C3A
|
D:HEM501
|
4.2
|
55.4
|
1.0
|
C2A
|
D:HEM501
|
4.2
|
54.7
|
1.0
|
C2B
|
D:HEM501
|
4.3
|
51.6
|
1.0
|
C3D
|
D:HEM501
|
4.3
|
45.9
|
1.0
|
C2D
|
D:HEM501
|
4.3
|
48.5
|
1.0
|
C3B
|
D:HEM501
|
4.3
|
49.6
|
1.0
|
C3C
|
D:HEM501
|
4.3
|
53.3
|
1.0
|
C2C
|
D:HEM501
|
4.3
|
51.4
|
1.0
|
CB
|
D:ALA264
|
4.4
|
54.4
|
1.0
|
N
|
D:ALA264
|
4.7
|
52.8
|
1.0
|
C13
|
D:BBJ502
|
4.9
|
57.8
|
1.0
|
|
Reference:
S.Luo,
K.Xu,
S.Xiang,
J.Chen,
C.Chen,
C.Guo,
Y.Tong,
L.Tong.
High-Resolution Structures of Inhibitor Complexes of Human Indoleamine 2,3-Dioxygenase 1 in A New Crystal Form. Acta Crystallogr F Struct V. 74 717 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30387777
DOI: 10.1107/S2053230X18012955
Page generated: Tue Aug 6 17:13:29 2024
|