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LIP_BURCE_45_364

Triacylglycerol lipase [AB hydrolase superfamily. Pseudomonas lipase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (LIP_BURCE):D: AB hydrolase-1 (60:62, 67, 71, 73, 130:132, 157, 161, 163, 164, 190, 208, 211)
291, 292, 295, 310, 311, 330, 331, 334, 336, 337
60:62, 67, 71, 73, 130:132, 157, 161, 163, 164, 190, 208, 211, 291, 292, 295, 310, 311, 330, 331, 334, 336, 337
Metals (Me):Ca

Full PDB list

1hqd, 1oil, 1ys1, 1ys2, 2lip, 2nw6, 3lip, 4lip, 5lip (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
G
6
0
L
6
1
S
6
2
Y
6
7
L
7
1
Y
7
3
H
1
3
0
S
1
3
1
Q
1
3
2
P
1
5
7
S
1
6
1
F
1
6
3
A
1
6
4
F
1
9
0
L
2
0
8
L
2
1
1
A
2
9
1
L
2
9
2
T
2
9
5
L
3
1
0
V
3
1
1
H
3
3
0
L
3
3
1
Q
3
3
6
L
3
3
7
[1]1hqd.a ink15 . . T . . . . * . . . . . . . . . . . V . . . . . Ca
[1]1ys1.x 2hr19 . . T . . . . * . . . . . . . . . . . V . . . . . Ca
[1]1ys2.x 2hs19 . . T . . . . * . . . . . . . . . . . V . . . . . Ca
[1]2nw6.a pot15 . . T . . . . * . . . . . . . . . . . V . . . . . Ca
[1]3lip.a none . . T . . . . . . . . . . . . . . . . V . . . . . Ca
[1]4lip.e ccp7 . . T . . . . * . . . . . . . . . . . V . . . . . Ca
[1]5lip.a ocp38 . . T . . . . * . . . . . . . . . . . V . . . . . Ca

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 Me
G
6
0
L
6
1
S
6
2
Y
6
7
L
7
1
Y
7
3
H
1
3
0
S
1
3
1
Q
1
3
2
P
1
5
7
S
1
6
1
F
1
6
3
A
1
6
4
F
1
9
0
L
2
0
8
L
2
1
1
A
2
9
1
L
2
9
2
T
2
9
5
L
3
1
0
V
3
1
1
H
3
3
0
L
3
3
1
I
3
3
4
Q
3
3
6
L
3
3
7
[1]1hqd.a . . T . . . . * . . . . . . . . . . . V . . . . . . Ca
[1]1ys1.x . . T . . . . * . . . . . . . . . . . V . . . . . . Ca
[1]1ys2.x . . T . . . . * . . . . . . . . . . . V . . . . . . Ca
[1]2nw6.a . . T . . . . * . . . . . . . . . . . V . . . . . . Ca
[1]3lip.a . . T . . . . * . . . . . . . . . . . V . . . . . . Ca
[1]4lip.e . . T . . . . * . . . . . . . . . . . V . . . . . . Ca
[1]5lip.a . . T . . . . * . . . . . . . . . . . V . . . . . . Ca

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
1hqd.a:ink
1ys1.x:2hr
1ys2.x:2hs
2nw6.a:pot
3lip.a is apo
4lip.e:ccp
5lip.a:ocp
[1] 1hqd.a
0.6
0.9 0.9 0.4 - 0.9 0.7
[1] 1ys1.x 0.7
0.6
0.6 0.4 - 0.6 0.6
[1] 1ys2.x 0.7 0.4
0.6
0.4 - 0.6 0.6
[1] 2nw6.a 0.7 0.6 0.6
0.6
- 0.6 0.8
[1] 3lip.a 0.7 0.6 0.6 0.6
-
0.6 0.6
[1] 4lip.e 0.7 0.5 0.5 0.5 -
0.6
0.7
[1] 5lip.a 0.6 0.5 0.7 0.4 - 0.7
0.8
[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
1hqd.a
1ys1.x
1ys2.x
2nw6.a
3lip.a
4lip.e
5lip.a
[1] 1hqd.a
0
.02 .02 .02 .02 .02 .03
[1] 1ys1.x .02
0
0 .01 0 0 .01
[1] 1ys2.x .02 0
0
.01 0 0 .01
[1] 2nw6.a .02 .01 .01
0
.01 .01 0
[1] 3lip.a .02 0 0 .01
0
0 .01
[1] 4lip.e .02 0 0 .01 0
0
.02
[1] 5lip.a .03 .01 .01 0 .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1hqd.a
1ys1.x
1ys2.x
2nw6.a
3lip.a
4lip.e
5lip.a
[1] 1hqd.a
0
0.2 0.2 0.3 0.2 0.2 0.4
[1] 1ys1.x 0.2
0
0.1 0.3 0.2 0.2 0.4
[1] 1ys2.x 0.2 0.1
0
0.3 0.2 0.2 0.4
[1] 2nw6.a 0.3 0.3 0.3
0
0.3 0.3 0.2
[1] 3lip.a 0.2 0.2 0.2 0.3
0
0.2 0.4
[1] 4lip.e 0.2 0.2 0.2 0.3 0.2
0
0.4
[1] 5lip.a 0.4 0.4 0.4 0.2 0.4 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1hqd.a
1ys1.x
1ys2.x
2nw6.a
3lip.a
4lip.e
5lip.a
[1] 1hqd.a
0
0.5 0.5 0.4 0.4 0.4 0.6
[1] 1ys1.x 0.5
0
0.1 0.5 0.5 0.5 0.4
[1] 1ys2.x 0.5 0.1
0
0.5 0.5 0.5 0.4
[1] 2nw6.a 0.4 0.5 0.5
0
0.4 0.3 0.5
[1] 3lip.a 0.4 0.5 0.5 0.4
0
0.3 0.6
[1] 4lip.e 0.4 0.5 0.5 0.3 0.3
0
0.5
[1] 5lip.a 0.6 0.4 0.4 0.5 0.6 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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