Fluorine in PDB 5v0w: Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088
Enzymatic activity of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088
All present enzymatic activity of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088:
2.3.1.97;
Protein crystallography data
The structure of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088, PDB code: 5v0w
was solved by
Seattle Structural Genomics Center For Infectious Disease (Ssgcid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.58 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.320,
119.130,
176.610,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.7 /
18.4
|
Other elements in 5v0w:
The structure of Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088
(pdb code 5v0w). 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 Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088, PDB code: 5v0w:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 5v0w
Go back to
Fluorine Binding Sites List in 5v0w
Fluorine binding site 1 out
of 6 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088
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 Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F502
b:11.2
occ:1.00
|
FAY
|
A:KFK502
|
0.0
|
11.2
|
1.0
|
CAN
|
A:KFK502
|
1.4
|
11.2
|
1.0
|
CAO
|
A:KFK502
|
2.3
|
8.7
|
1.0
|
CAM
|
A:KFK502
|
2.4
|
10.0
|
1.0
|
FAX
|
A:KFK502
|
2.7
|
12.5
|
1.0
|
N
|
A:ALA366
|
3.0
|
6.4
|
1.0
|
C
|
A:ASN365
|
3.2
|
10.6
|
1.0
|
CB
|
A:ASN365
|
3.3
|
7.4
|
1.0
|
C
|
A:ALA366
|
3.3
|
8.5
|
1.0
|
CA
|
A:ALA366
|
3.3
|
7.4
|
1.0
|
O
|
A:HOH654
|
3.4
|
16.0
|
1.0
|
O
|
A:ALA366
|
3.6
|
8.3
|
1.0
|
O
|
A:ASN365
|
3.6
|
11.3
|
1.0
|
CAP
|
A:KFK502
|
3.6
|
6.3
|
1.0
|
CAI
|
A:KFK502
|
3.6
|
7.8
|
1.0
|
N
|
A:LEU367
|
3.7
|
5.7
|
1.0
|
CA
|
A:ASN365
|
3.8
|
6.1
|
1.0
|
CD2
|
A:TYR334
|
3.9
|
7.9
|
1.0
|
CB
|
A:TYR211
|
4.0
|
9.7
|
1.0
|
CE2
|
A:TYR334
|
4.1
|
7.8
|
1.0
|
CG
|
A:LEU367
|
4.1
|
8.2
|
1.0
|
CAQ
|
A:KFK502
|
4.1
|
7.3
|
1.0
|
O
|
A:TYR212
|
4.5
|
8.6
|
1.0
|
CG
|
A:ASN365
|
4.5
|
13.2
|
1.0
|
O
|
A:HOH643
|
4.5
|
26.5
|
1.0
|
CA
|
A:LEU367
|
4.6
|
8.3
|
1.0
|
CD2
|
A:LEU367
|
4.6
|
7.9
|
1.0
|
OAH
|
A:KFK502
|
4.8
|
11.7
|
1.0
|
CA
|
A:TYR211
|
4.9
|
9.1
|
1.0
|
O
|
A:HOH835
|
4.9
|
8.6
|
1.0
|
CB
|
A:ALA366
|
4.9
|
8.7
|
1.0
|
CG
|
A:TYR334
|
4.9
|
6.6
|
1.0
|
CB
|
A:LEU367
|
4.9
|
6.8
|
1.0
|
CD1
|
A:LEU367
|
5.0
|
8.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 5v0w
Go back to
Fluorine Binding Sites List in 5v0w
Fluorine binding site 2 out
of 6 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088
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 Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F502
b:12.5
occ:1.00
|
FAX
|
A:KFK502
|
0.0
|
12.5
|
1.0
|
CAM
|
A:KFK502
|
1.4
|
10.0
|
1.0
|
CAN
|
A:KFK502
|
2.4
|
11.2
|
1.0
|
CAI
|
A:KFK502
|
2.4
|
7.8
|
1.0
|
FAY
|
A:KFK502
|
2.7
|
11.2
|
1.0
|
OAH
|
A:KFK502
|
2.8
|
11.7
|
1.0
|
CE1
|
A:HIS213
|
3.2
|
11.2
|
1.0
|
CB
|
A:TYR211
|
3.2
|
9.7
|
1.0
|
CB
|
A:ASN365
|
3.4
|
7.4
|
1.0
|
CAG
|
A:KFK502
|
3.5
|
12.5
|
1.0
|
ND1
|
A:HIS213
|
3.6
|
8.7
|
1.0
|
CAO
|
A:KFK502
|
3.6
|
8.7
|
1.0
|
CG
|
A:ASN365
|
3.7
|
13.2
|
1.0
|
CAQ
|
A:KFK502
|
3.7
|
7.3
|
1.0
|
CG
|
A:TYR211
|
3.7
|
10.8
|
1.0
|
CD1
|
A:TYR211
|
3.9
|
13.4
|
1.0
|
ND2
|
A:ASN365
|
4.1
|
11.8
|
1.0
|
OD1
|
A:ASN365
|
4.1
|
9.9
|
1.0
|
CAP
|
A:KFK502
|
4.1
|
6.3
|
1.0
|
CE2
|
A:TYR334
|
4.2
|
7.8
|
1.0
|
O
|
A:TYR212
|
4.2
|
8.6
|
1.0
|
NE2
|
A:HIS213
|
4.2
|
10.2
|
1.0
|
CA
|
A:ASN365
|
4.3
|
6.1
|
1.0
|
CAF
|
A:KFK502
|
4.4
|
8.0
|
1.0
|
CA
|
A:TYR211
|
4.5
|
9.1
|
1.0
|
N
|
A:ALA366
|
4.5
|
6.4
|
1.0
|
N
|
A:TYR212
|
4.6
|
8.0
|
1.0
|
CD2
|
A:TYR211
|
4.7
|
8.7
|
1.0
|
C
|
A:ASN365
|
4.7
|
10.6
|
1.0
|
C
|
A:TYR211
|
4.7
|
7.0
|
1.0
|
CD2
|
A:TYR334
|
4.7
|
7.9
|
1.0
|
O
|
A:ALA366
|
4.8
|
8.3
|
1.0
|
CG
|
A:HIS213
|
4.8
|
9.3
|
1.0
|
CZ
|
A:TYR334
|
4.9
|
7.7
|
1.0
|
C
|
A:TYR212
|
4.9
|
6.9
|
1.0
|
OH
|
A:TYR334
|
4.9
|
12.2
|
1.0
|
CAR
|
A:KFK502
|
5.0
|
13.0
|
1.0
|
CE1
|
A:TYR211
|
5.0
|
13.2
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 5v0w
Go back to
Fluorine Binding Sites List in 5v0w
Fluorine binding site 3 out
of 6 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088
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 Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F502
b:12.4
occ:1.00
|
FAY
|
B:KFK502
|
0.0
|
12.4
|
1.0
|
CAN
|
B:KFK502
|
1.3
|
11.2
|
1.0
|
CAM
|
B:KFK502
|
2.3
|
11.0
|
1.0
|
CAO
|
B:KFK502
|
2.4
|
9.2
|
1.0
|
FAX
|
B:KFK502
|
2.7
|
10.0
|
1.0
|
N
|
B:ALA366
|
2.9
|
8.2
|
1.0
|
C
|
B:ASN365
|
3.2
|
12.5
|
1.0
|
C
|
B:ALA366
|
3.2
|
10.5
|
1.0
|
CA
|
B:ALA366
|
3.2
|
7.0
|
1.0
|
CB
|
B:ASN365
|
3.3
|
8.2
|
1.0
|
O
|
B:HOH700
|
3.5
|
21.5
|
1.0
|
O
|
B:ALA366
|
3.5
|
8.4
|
1.0
|
CAI
|
B:KFK502
|
3.6
|
10.5
|
1.0
|
CAP
|
B:KFK502
|
3.6
|
10.2
|
1.0
|
O
|
B:ASN365
|
3.7
|
11.2
|
1.0
|
N
|
B:LEU367
|
3.7
|
9.6
|
1.0
|
CA
|
B:ASN365
|
3.8
|
8.0
|
1.0
|
CD2
|
B:TYR334
|
4.0
|
6.9
|
1.0
|
CB
|
B:TYR211
|
4.0
|
11.1
|
1.0
|
CAQ
|
B:KFK502
|
4.1
|
8.9
|
1.0
|
CE2
|
B:TYR334
|
4.2
|
10.6
|
1.0
|
CG
|
B:LEU367
|
4.2
|
7.8
|
1.0
|
O
|
B:TYR212
|
4.4
|
7.7
|
1.0
|
O
|
B:HOH693
|
4.4
|
22.6
|
1.0
|
CG
|
B:ASN365
|
4.5
|
12.9
|
1.0
|
CA
|
B:LEU367
|
4.6
|
8.3
|
1.0
|
CD2
|
B:LEU367
|
4.6
|
6.0
|
1.0
|
OAH
|
B:KFK502
|
4.7
|
12.0
|
1.0
|
CB
|
B:ALA366
|
4.8
|
6.5
|
1.0
|
CA
|
B:TYR211
|
4.8
|
11.0
|
1.0
|
CG
|
B:TYR334
|
4.9
|
7.3
|
1.0
|
N
|
B:TYR212
|
4.9
|
9.6
|
1.0
|
CB
|
B:LEU367
|
5.0
|
7.4
|
1.0
|
O
|
B:HOH922
|
5.0
|
9.3
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 5v0w
Go back to
Fluorine Binding Sites List in 5v0w
Fluorine binding site 4 out
of 6 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088
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 Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F502
b:10.0
occ:1.00
|
FAX
|
B:KFK502
|
0.0
|
10.0
|
1.0
|
CAM
|
B:KFK502
|
1.4
|
11.0
|
1.0
|
CAN
|
B:KFK502
|
2.4
|
11.2
|
1.0
|
CAI
|
B:KFK502
|
2.4
|
10.5
|
1.0
|
FAY
|
B:KFK502
|
2.7
|
12.4
|
1.0
|
OAH
|
B:KFK502
|
2.7
|
12.0
|
1.0
|
CE1
|
B:HIS213
|
3.2
|
12.0
|
1.0
|
CB
|
B:TYR211
|
3.2
|
11.1
|
1.0
|
CB
|
B:ASN365
|
3.4
|
8.2
|
1.0
|
CAG
|
B:KFK502
|
3.5
|
12.6
|
1.0
|
ND1
|
B:HIS213
|
3.6
|
11.3
|
1.0
|
CG
|
B:ASN365
|
3.6
|
12.9
|
1.0
|
CAO
|
B:KFK502
|
3.6
|
9.2
|
1.0
|
CAQ
|
B:KFK502
|
3.7
|
8.9
|
1.0
|
CG
|
B:TYR211
|
3.8
|
7.5
|
1.0
|
ND2
|
B:ASN365
|
3.9
|
16.6
|
1.0
|
CD2
|
B:TYR211
|
4.0
|
9.1
|
1.0
|
OD1
|
B:ASN365
|
4.0
|
12.8
|
1.0
|
CAP
|
B:KFK502
|
4.1
|
10.2
|
1.0
|
O
|
B:TYR212
|
4.1
|
7.7
|
1.0
|
CE2
|
B:TYR334
|
4.2
|
10.6
|
1.0
|
NE2
|
B:HIS213
|
4.3
|
14.7
|
1.0
|
CA
|
B:ASN365
|
4.3
|
8.0
|
1.0
|
CAF
|
B:KFK502
|
4.3
|
11.0
|
1.0
|
N
|
B:ALA366
|
4.5
|
8.2
|
1.0
|
CA
|
B:TYR211
|
4.5
|
11.0
|
1.0
|
N
|
B:TYR212
|
4.5
|
9.6
|
1.0
|
C
|
B:ASN365
|
4.7
|
12.5
|
1.0
|
CD1
|
B:TYR211
|
4.7
|
8.7
|
1.0
|
C
|
B:TYR211
|
4.7
|
12.7
|
1.0
|
O
|
B:ALA366
|
4.7
|
8.4
|
1.0
|
CD2
|
B:TYR334
|
4.8
|
6.9
|
1.0
|
CG
|
B:HIS213
|
4.8
|
10.7
|
1.0
|
C
|
B:TYR212
|
4.9
|
8.0
|
1.0
|
CZ
|
B:TYR334
|
4.9
|
7.8
|
1.0
|
OH
|
B:TYR334
|
4.9
|
9.2
|
1.0
|
CAR
|
B:KFK502
|
5.0
|
11.5
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 5v0w
Go back to
Fluorine Binding Sites List in 5v0w
Fluorine binding site 5 out
of 6 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088
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 Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F502
b:11.7
occ:1.00
|
FAY
|
C:KFK502
|
0.0
|
11.7
|
1.0
|
CAN
|
C:KFK502
|
1.3
|
9.2
|
1.0
|
CAO
|
C:KFK502
|
2.3
|
8.0
|
1.0
|
CAM
|
C:KFK502
|
2.4
|
8.4
|
1.0
|
FAX
|
C:KFK502
|
2.7
|
10.9
|
1.0
|
N
|
C:ALA366
|
3.1
|
7.4
|
1.0
|
C
|
C:ASN365
|
3.3
|
8.6
|
1.0
|
CB
|
C:ASN365
|
3.3
|
8.3
|
1.0
|
C
|
C:ALA366
|
3.3
|
6.7
|
1.0
|
CA
|
C:ALA366
|
3.4
|
6.7
|
1.0
|
O
|
C:HOH690
|
3.4
|
21.2
|
1.0
|
O
|
C:ALA366
|
3.5
|
9.3
|
1.0
|
CAP
|
C:KFK502
|
3.6
|
9.4
|
1.0
|
CAI
|
C:KFK502
|
3.6
|
8.2
|
1.0
|
O
|
C:ASN365
|
3.6
|
10.5
|
1.0
|
N
|
C:LEU367
|
3.7
|
6.7
|
1.0
|
CA
|
C:ASN365
|
3.8
|
7.2
|
1.0
|
CB
|
C:TYR211
|
4.0
|
8.5
|
1.0
|
CD2
|
C:TYR334
|
4.0
|
9.8
|
1.0
|
CG
|
C:LEU367
|
4.1
|
7.0
|
1.0
|
CAQ
|
C:KFK502
|
4.1
|
6.9
|
1.0
|
CE2
|
C:TYR334
|
4.3
|
8.9
|
1.0
|
O
|
C:HOH676
|
4.4
|
16.8
|
1.0
|
CD2
|
C:LEU367
|
4.4
|
8.1
|
1.0
|
O
|
C:TYR212
|
4.5
|
10.6
|
1.0
|
CG
|
C:ASN365
|
4.5
|
13.4
|
1.0
|
CA
|
C:LEU367
|
4.6
|
6.5
|
1.0
|
OAH
|
C:KFK502
|
4.7
|
8.2
|
1.0
|
CA
|
C:TYR211
|
4.8
|
7.3
|
1.0
|
CB
|
C:ALA366
|
4.9
|
6.7
|
1.0
|
CB
|
C:LEU367
|
4.9
|
6.3
|
1.0
|
N
|
C:TYR212
|
4.9
|
7.8
|
1.0
|
O
|
C:HOH872
|
5.0
|
9.3
|
1.0
|
CG
|
C:TYR334
|
5.0
|
6.9
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 5v0w
Go back to
Fluorine Binding Sites List in 5v0w
Fluorine binding site 6 out
of 6 in the Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088
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 Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F502
b:10.9
occ:1.00
|
FAX
|
C:KFK502
|
0.0
|
10.9
|
1.0
|
CAM
|
C:KFK502
|
1.4
|
8.4
|
1.0
|
CAN
|
C:KFK502
|
2.4
|
9.2
|
1.0
|
CAI
|
C:KFK502
|
2.4
|
8.2
|
1.0
|
FAY
|
C:KFK502
|
2.7
|
11.7
|
1.0
|
OAH
|
C:KFK502
|
2.7
|
8.2
|
1.0
|
CE1
|
C:HIS213
|
3.1
|
13.9
|
1.0
|
CB
|
C:ASN365
|
3.3
|
8.3
|
1.0
|
CB
|
C:TYR211
|
3.3
|
8.5
|
1.0
|
ND1
|
C:HIS213
|
3.5
|
9.3
|
1.0
|
CAG
|
C:KFK502
|
3.5
|
9.8
|
1.0
|
CG
|
C:ASN365
|
3.6
|
13.4
|
1.0
|
CAO
|
C:KFK502
|
3.6
|
8.0
|
1.0
|
CAQ
|
C:KFK502
|
3.6
|
6.9
|
1.0
|
CG
|
C:TYR211
|
3.8
|
9.1
|
1.0
|
OD1
|
C:ASN365
|
4.0
|
11.3
|
1.0
|
CD1
|
C:TYR211
|
4.0
|
9.2
|
1.0
|
CAP
|
C:KFK502
|
4.1
|
9.4
|
1.0
|
ND2
|
C:ASN365
|
4.1
|
15.0
|
1.0
|
CE2
|
C:TYR334
|
4.2
|
8.9
|
1.0
|
O
|
C:TYR212
|
4.2
|
10.6
|
1.0
|
NE2
|
C:HIS213
|
4.3
|
12.4
|
1.0
|
CA
|
C:ASN365
|
4.3
|
7.2
|
1.0
|
CAF
|
C:KFK502
|
4.4
|
9.8
|
1.0
|
N
|
C:ALA366
|
4.5
|
7.4
|
1.0
|
CA
|
C:TYR211
|
4.6
|
7.3
|
1.0
|
N
|
C:TYR212
|
4.6
|
7.8
|
1.0
|
C
|
C:ASN365
|
4.7
|
8.6
|
1.0
|
CD2
|
C:TYR211
|
4.7
|
13.4
|
1.0
|
CD2
|
C:TYR334
|
4.7
|
9.8
|
1.0
|
C
|
C:TYR211
|
4.8
|
7.7
|
1.0
|
CG
|
C:HIS213
|
4.8
|
8.4
|
1.0
|
O
|
C:ALA366
|
4.8
|
9.3
|
1.0
|
C
|
C:TYR212
|
4.9
|
8.3
|
1.0
|
CAR
|
C:KFK502
|
4.9
|
10.0
|
1.0
|
CZ
|
C:TYR334
|
5.0
|
7.5
|
1.0
|
|
Reference:
S.J.Mayclin,
J.Abendroth,
D.D.Lorimer,
T.E.Edwards.
Crystal Structure of Glycylpeptide N-Tetradecanoyltransferase From Plasmodium Vivax in Complex with Inhibitor Imp-0001088 To Be Published.
Page generated: Thu Aug 1 15:54:44 2024
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