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OBP_BOVIN_1_159

Odorant-binding protein [Calycin superfamily. Lipocalin family]

Composition of the binding site

Protein chains monomer
A1 (OBP_BOVIN):22, 36, 38, 40, 54, 56, 69, 81, 83, 87, 89, 101:103, 115:117, 11922, 36, 38, 40, 54, 56, 69, 81, 83, 87, 89, 101:103, 115:117, 119

Full PDB list

1g85, 1gt1, 1gt3, 1gt4, 1gt5, 1hn2, 1obp, 1pbo, 2hlv

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
2
2
F
3
6
T
3
8
F
4
0
F
5
4
F
5
6
V
6
9
A
8
1
Y
8
3
N
8
7
F
8
9
A
1
0
1
H
1
0
2
N
1
0
3
L
1
1
5
T
1
1
6
E
1
1
7
F
1
1
9
[1]1g85.b 3ol,3ol18 . . . . . . . . . . . . . . . . G .
[1]1gt1.a anc,prz27 . . . . . . . . . . . . . . . . . .
[1]1gt1.b 3om,anc24 . . . . . . . . . . . . . . . . . .
[1]1gt3.a 3om,dhm20 . . . . . . . . . . . . . . . . . .
[1]1gt4.a una12 . . . . . . . . . . . . . . . . . .
[1]1gt5.a bzq14 . . . . . . . . . . . . . . . . . .
[1]1hn2.a anc15 . . . . . . . . . . . . . . . . . .
[1]1hn2.b 3ol,anc24 . . . . . . . . . . . . . . . . . .
[1]1obp.a none . . . . . . . . . . . . . . . . G .
[1]1pbo.a ses13 . . . . . . . . . . . . . . . . G .
[1]2hlv.a lik14 . . . . . . . . . . . . . . . . . .

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
I
2
2
F
3
6
T
3
8
F
4
0
F
5
4
F
5
6
V
6
9
A
8
1
Y
8
3
N
8
7
F
8
9
A
1
0
1
H
1
0
2
N
1
0
3
L
1
1
5
T
1
1
6
E
1
1
7
F
1
1
9
[1]1g85.b . . . . . . . . . . * . . . . . G .
[1]1gt1.a . . . . . . . . . . . . . . . . . .
[1]1gt1.b . . . . . . . . . . * . . . . . . .
[1]1gt3.a . . . . . . . . . . * . . . . . . .
[1]1gt4.a . . . . . . . . . . . . . . . . . .
[1]1gt5.a . . . . . . . . . . * . . . . . . .
[1]1hn2.a . . . . . . . . . . . . . . . . . .
[1]1hn2.b . . . . . . . . . . * . . . . . . .
[1]1obp.a . . . . . . . . . . * . . . . . G .
[1]1pbo.a . . . . . . . . . . . . . . . . G .
[1]2hlv.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
1g85.b:3ol
1gt1.a:anc,prz
1gt1.b:3om,anc
1gt3.a:3om,dhm
1gt4.a:una
1gt5.a:bzq
1hn2.a:anc
1hn2.b:3ol,anc
1obp.a is apo
1pbo.a:ses
2hlv.a:lik
[1] 1g85.b
0
1.2 0.3 0 0.2 0.1 0.2 0.2 - 2.7 2.2
[1] 1gt1.a 0.1
0
0.1 0 0 0 0 0 - 0.2 0.3
[1] 1gt1.b 0 1.2
0.1
0 0.1 0 0 0 - 2.1 1.7
[1] 1gt3.a 0 1.2 0.1
0
0.2 0 0 0.1 - 2.6 2.3
[1] 1gt4.a 0 0 0.2 0
0
0 0 0.1 - 0.2 0.3
[1] 1gt5.a 0.2 0.7 0.3 0 0.1
0
0 0 - 1.5 1.3
[1] 1hn2.a 0.1 0 0 0 0 0
0
0 - 0.3 0.3
[1] 1hn2.b 0 1.2 0.2 0 0.2 0 0
0.1
- 2.5 2.0
[1] 1obp.a 0 1.2 0.3 0 0.2 0.1 0.1 0.2
-
2.6 2.2
[1] 1pbo.a 0 0 0.1 0 0 0 0 0.1 -
0.1
0.3
[1] 2hlv.a 0.1 0 0.2 0 0 0 0 0 - 0.1
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
1g85.b
1gt1.a
1gt1.b
1gt3.a
1gt4.a
1gt5.a
1hn2.a
1hn2.b
1obp.a
1pbo.a
2hlv.a
[1] 1g85.b
0
.15 .04 .01 .14 .09 .14 .02 .01 .14 .18
[1] 1gt1.a .15
0
.11 .15 .02 .08 .01 .13 .14 .02 .03
[1] 1gt1.b .04 .11
0
.05 .11 .05 .11 .02 .04 .12 .14
[1] 1gt3.a .01 .15 .05
0
.16 .08 .14 .03 .01 .14 .18
[1] 1gt4.a .14 .02 .11 .16
0
.10 .03 .13 .14 .01 .03
[1] 1gt5.a .09 .08 .05 .08 .10
0
.08 .07 .08 .10 .11
[1] 1hn2.a .14 .01 .11 .14 .03 .08
0
.13 .14 .02 .04
[1] 1hn2.b .02 .13 .02 .03 .13 .07 .13
0
.02 .14 .16
[1] 1obp.a .01 .14 .04 .01 .14 .08 .14 .02
0
.14 .17
[1] 1pbo.a .14 .02 .12 .14 .01 .10 .02 .14 .14
0
.03
[1] 2hlv.a .18 .03 .14 .18 .03 .11 .04 .16 .17 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1g85.b
1gt1.a
1gt1.b
1gt3.a
1gt4.a
1gt5.a
1hn2.a
1hn2.b
1obp.a
1pbo.a
2hlv.a
[1] 1g85.b
0
0.2 0.1 0.1 0.2 0.2 0.2 0.1 0.2 0.2 0.4
[1] 1gt1.a 0.2
0
0.1 0.1 0.1 0.1 0.1 0.2 0.1 0.2 0.3
[1] 1gt1.b 0.1 0.1
0
0.1 0.2 0.2 0.2 0 0.2 0.2 0.4
[1] 1gt3.a 0.1 0.1 0.1
0
0.2 0.1 0.1 0.1 0.1 0.2 0.4
[1] 1gt4.a 0.2 0.1 0.2 0.2
0
0.2 0.1 0.2 0.2 0.2 0.3
[1] 1gt5.a 0.2 0.1 0.2 0.1 0.2
0
0.1 0.2 0.1 0.2 0.4
[1] 1hn2.a 0.2 0.1 0.2 0.1 0.1 0.1
0
0.2 0.1 0.2 0.4
[1] 1hn2.b 0.1 0.2 0 0.1 0.2 0.2 0.2
0
0.2 0.2 0.4
[1] 1obp.a 0.2 0.1 0.2 0.1 0.2 0.1 0.1 0.2
0
0.2 0.4
[1] 1pbo.a 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
0
0.3
[1] 2hlv.a 0.4 0.3 0.4 0.4 0.3 0.4 0.4 0.4 0.4 0.3
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
1g85.b
1gt1.a
1gt1.b
1gt3.a
1gt4.a
1gt5.a
1hn2.a
1hn2.b
1obp.a
1pbo.a
2hlv.a
[1] 1g85.b
0
0.7 0.2 0.5 0.8 0.7 0.8 0.1 0.9 1.0 0.9
[1] 1gt1.a 0.7
0
0.7 0.5 0.4 0.5 0.4 0.7 0.9 0.8 0.9
[1] 1gt1.b 0.2 0.7
0
0.5 0.7 0.6 0.7 0.1 0.9 1.0 0.9
[1] 1gt3.a 0.5 0.5 0.5
0
0.6 0.4 0.5 0.5 0.8 0.9 1.0
[1] 1gt4.a 0.8 0.4 0.7 0.6
0
0.5 0.2 0.8 0.9 0.9 0.8
[1] 1gt5.a 0.7 0.5 0.6 0.4 0.5
0
0.4 0.6 0.8 1.0 0.9
[1] 1hn2.a 0.8 0.4 0.7 0.5 0.2 0.4
0
0.7 0.8 0.9 0.8
[1] 1hn2.b 0.1 0.7 0.1 0.5 0.8 0.6 0.7
0
0.9 1.0 0.9
[1] 1obp.a 0.9 0.9 0.9 0.8 0.9 0.8 0.8 0.9
0
0.8 1.2
[1] 1pbo.a 1.0 0.8 1.0 0.9 0.9 1.0 0.9 1.0 0.8
0
1.1
[1] 2hlv.a 0.9 0.9 0.9 1.0 0.8 0.9 0.8 0.9 1.2 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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