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LIP_THELA_23_291

Lipase [AB hydrolase superfamily. Lipase family]

Composition of the binding site

Protein chains monomer
A1 (LIP_THELA):83:86, 103:117, 132, 134, 135, 169, 17383:86, 103:117, 132, 134, 135, 169, 173

Full PDB list

1dt3, 1dt5, 1dte, 1du4, 1ein, 1gt6, 1tib, 4dyh, 4ea6, 4flf, 4gbg, 4ghw, 4gi1, 4glb, 4gwl, 4kjx, 4n8s, 4s0x, 4zgb, 5ap9 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
G
8
3
D
8
4
V
8
5
T
8
6
R
1
0
3
G
1
0
4
S
1
0
5
R
1
0
6
S
1
0
7
N
1
1
0
W
1
1
1
N
1
1
4
L
1
1
5
N
1
1
6
H
1
3
2
L
1
6
9
L
1
7
3
[1]4ghw.a dka12 . . . . . . . . . . . . . . . . .
[1]4gi1.a 16y19 . . . . . . . . . . . . . . . . .
[1]4glb.a xxh11 . . . . . . . . . . . . . . . . .
[1]4kjx.a dao14 . . . . . . . . . . . . . . . . .
[1]4n8s.a eac9 . . . . . . . . . . . . . . . . .
[1]5ap9.b none . . . . . . . . . . . . . . . . .
[2]1gt6.a none . . . . . . . . . . . . . . . . .

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

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PDB.ch
A1
G
8
3
D
8
4
V
8
5
T
8
6
R
1
0
3
G
1
0
4
S
1
0
5
R
1
0
6
S
1
0
7
I
1
0
8
E
1
0
9
N
1
1
0
W
1
1
1
I
1
1
2
G
1
1
3
N
1
1
4
L
1
1
5
N
1
1
6
F
1
1
7
H
1
3
2
G
1
3
4
F
1
3
5
L
1
6
9
L
1
7
3
[1]4ghw.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]4gi1.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]4glb.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]4kjx.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]4n8s.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ap9.b . . . . . . . . . C . . . . . * . . . . . . . .
[2]1gt6.a . . . . . . . . * . . * * * * * * * . . . . . .

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
4ghw.a:dka
4gi1.a:16y
4glb.a:xxh
4kjx.a:dao
4n8s.a:eac
5ap9.b is apo
1gt6.a is apo
[1] 4ghw.a
0
0 0 0.3 0.1 - -
[1] 4gi1.a 0
0.1
0.1 0.4 0.1 - -
[1] 4glb.a 0.1 0.1
0
0.2 0.1 - -
[1] 4kjx.a 0 0 0
0.1
0 - -
[1] 4n8s.a 0 0.1 0 0.1
0.2
- -
[1] 5ap9.b 1.1 2.2 0.4 0.3 0
-
-
[2] 1gt6.a 7.4 14 8.3 8.0 6.0 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
4ghw.a
4gi1.a
4glb.a
4kjx.a
4n8s.a
5ap9.b
1gt6.a
[1] 4ghw.a
0
.01 0 .01 .01 .10 .75
[1] 4gi1.a .01
0
0 .02 .02 .10 .74
[1] 4glb.a 0 0
0
.01 .02 .09 .75
[1] 4kjx.a .01 .02 .01
0
.01 .10 .76
[1] 4n8s.a .01 .02 .02 .01
0
.10 .75
[1] 5ap9.b .10 .10 .09 .10 .10
0
.70
[2] 1gt6.a .75 .74 .75 .76 .75 .70
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
4ghw.a
4gi1.a
4glb.a
4kjx.a
4n8s.a
5ap9.b
1gt6.a
[1] 4ghw.a
0
0.3 0.3 0.2 0.4 2.8 4.9
[1] 4gi1.a 0.3
0
0.2 0.2 0.4 2.8 5.0
[1] 4glb.a 0.3 0.2
0
0.2 0.4 2.8 4.9
[1] 4kjx.a 0.2 0.2 0.2
0
0.3 2.8 4.9
[1] 4n8s.a 0.4 0.4 0.4 0.3
0
2.8 4.9
[1] 5ap9.b 2.8 2.8 2.8 2.8 2.8
0
5.1
[2] 1gt6.a 4.9 5.0 4.9 4.9 4.9 5.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
4ghw.a
4gi1.a
4glb.a
4kjx.a
4n8s.a
5ap9.b
1gt6.a
[1] 4ghw.a
0
0.9 0.9 0.8 0.8 3.3 6.0
[1] 4gi1.a 0.9
0
0.3 0.7 0.7 3.3 6.1
[1] 4glb.a 0.9 0.3
0
0.6 0.8 3.4 6.0
[1] 4kjx.a 0.8 0.7 0.6
0
0.7 3.3 6.0
[1] 4n8s.a 0.8 0.7 0.8 0.7
0
3.4 6.0
[1] 5ap9.b 3.3 3.3 3.4 3.3 3.4
0
6.0
[2] 1gt6.a 6.0 6.1 6.0 6.0 6.0 6.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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