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PGES2_MACFA_88_377

Prostaglandin E synthase 2 [GST superfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PGES2_MACFA):D: Glutaredoxin (107, 109:112, 134, 137)
D: GST C-terminal (263, 264, 293, 343, 347)
243, 244, 246, 247, 250, 251, 260
107, 109:112, 134, 137, 243, 244, 246, 247, 250, 251, 260, 263, 264, 293, 343, 347
Cofactors (cF):gsh
Metals (Me):Fe

Full PDB list

1z9h, 2pbj

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
Y
1
0
7
T
1
0
9
C
1
1
0
P
1
1
1
F
1
1
2
P
1
3
4
R
1
3
7
V
2
4
3
H
2
4
4
I
2
4
6
S
2
4
7
V
2
5
0
Y
2
5
1
S
2
6
0
Y
2
6
3
I
2
6
4
L
2
9
3
V
3
4
3
L
3
4
7
[1]1z9h.a imn25 . . . . . . . . . . . . . . . . . . .
[1]2pbj.a hem42 . . . . . . . . . . . . . . . . . . . gsh Fe

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1 cF Me
Y
1
0
7
T
1
0
9
C
1
1
0
P
1
1
1
F
1
1
2
P
1
3
4
R
1
3
7
V
2
4
3
H
2
4
4
I
2
4
6
S
2
4
7
V
2
5
0
Y
2
5
1
S
2
6
0
Y
2
6
3
I
2
6
4
L
2
9
3
V
3
4
3
L
3
4
7
[1]1z9h.a . . . . . . . . . . . . . . . . . . .
[1]2pbj.a . . . . . . . . . . . . . . . . . . . gsh Fe

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1z9h.a:imn
2pbj.a:hem
[1] 1z9h.a
0
0
[1] 2pbj.a 0.2
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1z9h.a
2pbj.a
[1] 1z9h.a
0
.01
[1] 2pbj.a .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1z9h.a
2pbj.a
[1] 1z9h.a
0
0.2
[1] 2pbj.a 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1z9h.a
2pbj.a
[1] 1z9h.a
0
0.4
[1] 2pbj.a 0.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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