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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:

Chlorine (Cl) 5 atoms

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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