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OBP_PIG_2_157

Odorant-binding protein [Calycin superfamily. Lipocalin family]

Composition of the binding site

Protein chains monomer
A1 (OBP_PIG):21, 35, 37, 39, 42, 53, 55, 68, 80, 82, 86, 88, 100, 102, 114:116, 11821, 35, 37, 39, 42, 53, 55, 68, 80, 82, 86, 88, 100, 102, 114:116, 118

Full PDB list

1a3y, 1dzj, 1dzk, 1dzm, 1dzp, 1e00, 1e02, 1e06, 1hqp (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
2
1
F
3
5
V
3
7
M
3
9
L
5
3
F
5
5
L
6
8
V
8
0
Y
8
2
N
8
6
F
8
8
I
1
0
0
N
1
0
2
M
1
1
4
T
1
1
5
G
1
1
6
L
1
1
8
[1]1a3y.b none . . . . . . . . . . . . . . . . .
[1]1dzj.a ses13 . . . . . . . . . . . . . . . . .
[1]1dzk.a prz10 . . . . . . . . . . . . . . . . .
[1]1dzm.b bzm16 . . . . . . . . . . . . . . . . .
[1]1dzp.b bzq14 . . . . . . . . . . . . . . . . .
[1]1e00.b dhm11 . . . . . . . . . . . . . . . . .
[1]1e02.b una12 . . . . . . . . . . . . . . . . .
[1]1e06.b ipb11 . . . . . . . . . . . . . . . . .

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
I
2
1
F
3
5
V
3
7
M
3
9
I
4
2
L
5
3
F
5
5
L
6
8
V
8
0
Y
8
2
N
8
6
F
8
8
I
1
0
0
N
1
0
2
M
1
1
4
T
1
1
5
G
1
1
6
L
1
1
8
[1]1a3y.b . . . . . . . . . . . . . . . . . .
[1]1dzj.a . . . . . . . . . . . . . . . . . .
[1]1dzk.a . . . . . . . . . . . . . . . . . .
[1]1dzm.b . . . . . . . . . . . . . . . . . .
[1]1dzp.b . . . . . . . . . . . . . . . . . .
[1]1e00.b . . . . . . . . . . . . . . . . . .
[1]1e02.b . . . . . . . . . . . . . . . . . .
[1]1e06.b . . . . . . . . . . . . . . . . . .

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
1a3y.b is apo
1dzj.a:ses
1dzk.a:prz
1dzm.b:bzm
1dzp.b:bzq
1e00.b:dhm
1e02.b:una
1e06.b:ipb
[1] 1a3y.b
-
0.3 0.1 0.1 0 0 0.3 0
[1] 1dzj.a -
0
0 0.2 0 0 0.1 0
[1] 1dzk.a - 0
0
0.2 0 0 0.1 0
[1] 1dzm.b - 0.1 0
0
0 0 0.2 0
[1] 1dzp.b - 0.1 0 0
0
0 0.2 0
[1] 1e00.b - 0.1 0 0 0
0
0.2 0
[1] 1e02.b - 0.2 0.1 0.1 0 0
0.2
0
[1] 1e06.b - 0.1 0 0 0 0 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
1a3y.b
1dzj.a
1dzk.a
1dzm.b
1dzp.b
1e00.b
1e02.b
1e06.b
[1] 1a3y.b
0
.04 .04 .03 .03 .03 .01 .03
[1] 1dzj.a .04
0
0 .02 .02 .02 .03 .02
[1] 1dzk.a .04 0
0
.02 .02 .02 .03 .02
[1] 1dzm.b .03 .02 .02
0
0 0 .02 0
[1] 1dzp.b .03 .02 .02 0
0
0 .02 0
[1] 1e00.b .03 .02 .02 0 0
0
.02 0
[1] 1e02.b .01 .03 .03 .02 .02 .02
0
.02
[1] 1e06.b .03 .02 .02 0 0 0 .02
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
1a3y.b
1dzj.a
1dzk.a
1dzm.b
1dzp.b
1e00.b
1e02.b
1e06.b
[1] 1a3y.b
0
0.3 0.3 0.2 0.2 0.2 0.1 0.2
[1] 1dzj.a 0.3
0
0.1 0.2 0.2 0.2 0.2 0.2
[1] 1dzk.a 0.3 0.1
0
0.2 0.2 0.2 0.2 0.2
[1] 1dzm.b 0.2 0.2 0.2
0
0.1 0.1 0.2 0.1
[1] 1dzp.b 0.2 0.2 0.2 0.1
0
0.1 0.2 0.1
[1] 1e00.b 0.2 0.2 0.2 0.1 0.1
0
0.2 0.1
[1] 1e02.b 0.1 0.2 0.2 0.2 0.2 0.2
0
0.2
[1] 1e06.b 0.2 0.2 0.2 0.1 0.1 0.1 0.2
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

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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
1a3y.b
1dzj.a
1dzk.a
1dzm.b
1dzp.b
1e00.b
1e02.b
1e06.b
[1] 1a3y.b
0
0.7 0.8 0.7 0.7 0.7 0.2 0.5
[1] 1dzj.a 0.7
0
0.3 0.6 0.6 0.6 0.7 0.5
[1] 1dzk.a 0.8 0.3
0
0.7 0.6 0.6 0.7 0.6
[1] 1dzm.b 0.7 0.6 0.7
0
0.3 0.3 0.6 0.4
[1] 1dzp.b 0.7 0.6 0.6 0.3
0
0.1 0.7 0.5
[1] 1e00.b 0.7 0.6 0.6 0.3 0.1
0
0.7 0.5
[1] 1e02.b 0.2 0.7 0.7 0.6 0.7 0.7
0
0.5
[1] 1e06.b 0.5 0.5 0.6 0.4 0.5 0.5 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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