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PAG15_HUMAN_33_412

Group XV phospholipase A2 [AB hydrolase superfamily. Lipase family]

Composition of the binding site

Protein chains monomer
A1 (PAG15_HUMAN):45:47, 76, 77, 79, 82, 127, 134, 137, 163, 164, 197:199, 229, 233, 235, 236, 239, 247, 248, 259, 260, 263, 266, 269, 362, 363, 392, 39345:47, 76, 77, 79, 82, 127, 134, 137, 163, 164, 197:199, 229, 233, 235, 236, 239, 247, 248, 259, 260, 263, 266, 269, 362, 363, 392, 393

Full PDB list

4x90, 4x91, 4x92, 4x93, 4x94, 4x95, 4x97 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
4
5
D
4
6
L
4
7
W
7
6
L
7
9
L
8
2
L
1
2
7
Y
1
3
7
W
1
6
3
H
1
9
7
S
1
9
8
M
1
9
9
P
2
2
9
V
2
3
3
T
2
3
6
V
2
3
9
R
2
4
7
Q
2
5
9
Q
2
6
0
A
2
6
3
T
2
6
6
L
2
6
9
T
3
6
2
H
3
9
2
I
3
9
3
[1]4x90.a none . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x91.a ief19 . . . . . . . . . . * . . . . . . . . . . . . . .
[1]4x92.a none . . . . . . . . . . A . . . . . . . . . . . . . .
[1]4x97.c may19 . . . . . . . . . . * . . . . . . . . . . . . . .

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
G
4
5
D
4
6
L
4
7
W
7
6
L
7
7
L
7
9
L
8
2
L
1
2
7
V
1
3
4
Y
1
3
7
W
1
6
3
R
1
6
4
H
1
9
7
S
1
9
8
M
1
9
9
P
2
2
9
V
2
3
3
K
2
3
5
T
2
3
6
V
2
3
9
R
2
4
7
I
2
4
8
Q
2
5
9
Q
2
6
0
A
2
6
3
T
2
6
6
L
2
6
9
T
3
6
2
V
3
6
3
H
3
9
2
I
3
9
3
[1]4x90.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4x91.a . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]4x92.a . . . . . . . . . . . . . A . . . . . . * . . . . . . . . . .
[1]4x97.c . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .

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
4x90.a is apo
4x91.a:ief
4x92.a is apo
4x97.c:may
[1] 4x90.a
-
0.6 - 0.4
[1] 4x91.a -
0.7
- 0.6
[1] 4x92.a - 0.2
-
3.1
[1] 4x97.c - 0.6 -
0.6
[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
4x90.a
4x91.a
4x92.a
4x97.c
[1] 4x90.a
0
.01 .11 .01
[1] 4x91.a .01
0
.11 0
[1] 4x92.a .11 .11
0
.11
[1] 4x97.c .01 0 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
4x90.a
4x91.a
4x92.a
4x97.c
[1] 4x90.a
0
0.2 0.6 0.4
[1] 4x91.a 0.2
0
0.6 0.3
[1] 4x92.a 0.6 0.6
0
0.7
[1] 4x97.c 0.4 0.3 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue 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
4x90.a
4x91.a
4x92.a
4x97.c
[1] 4x90.a
0
0.5 0.8 0.5
[1] 4x91.a 0.5
0
1.0 0.6
[1] 4x92.a 0.8 1.0
0
0.9
[1] 4x97.c 0.5 0.6 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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