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HNL_HEVBR_1_257

(S)-hydroxynitrile lyase [AB hydrolase superfamily. Hydroxynitrile lyase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (HNL_HEVBR):D: AB hydrolase-1 (11, 12, 14, 80, 81, 121, 128, 148, 152, 157, 178, 209, 210, 235, 236)11, 12, 14, 80, 81, 121, 128, 148, 152, 157, 178, 209, 210, 235, 236

Full PDB list

1qj4, 1sc9, 1sci, 1sck, 1scq, 1yas, 1yb6, 1yb7, 2g4l, 2yas, 3c6x, 3c6y, 3c6z, 3c70, 3yas, 4yas, 5yas, 6yas, 7yas (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
1
1
I
1
2
H
1
4
S
8
0
C
8
1
L
1
2
1
W
1
2
8
L
1
4
8
L
1
5
2
L
1
5
7
I
2
0
9
F
2
1
0
H
2
3
5
K
2
3
6
[1]1sc9.a cnh6 . . . . . . . . . . . . . .
[1]1sck.a none . . . . . . . . . . . . . L
[1]1scq.a cnh6 . . . . . . . . . . . . . L
[1]1yas.a H11 . . . . . . . . . . . . . .
[1]1yb6.a mnn10 . . . . . . . . . . . . . .
[1]1yb7.a icn8 . . . . . . . . . . . . . .
[1]3c6x.a none . . . . . . . . . . . . . .
[1]4yas.a clx6 . . . * . . . . . . . . . .
[1]5yas.a fac11 . . . . . . . . . . . . . .

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
T
1
1
I
1
2
H
1
4
S
8
0
C
8
1
L
1
2
1
W
1
2
8
L
1
4
8
L
1
5
2
L
1
5
7
L
1
7
8
I
2
0
9
F
2
1
0
H
2
3
5
K
2
3
6
[1]1sc9.a . . . * . . . . . . . . . . .
[1]1sck.a . . . . . . . . . . . . . . L
[1]1scq.a . . . * . . . . . . . . . . L
[1]1yas.a . . . . . . . . . . . . . . .
[1]1yb6.a . . . * . . . . . . . . . . .
[1]1yb7.a . . . * . . . . . . . . . . .
[1]3c6x.a . . . * . . . . . . . . . . .
[1]4yas.a . . . * . . . . . . . . . . .
[1]5yas.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
1sc9.a:cnh
1sck.a is apo
1scq.a:cnh
1yas.a:H
1yb6.a:mnn
1yb7.a:icn
3c6x.a is apo
4yas.a:clx
5yas.a:fac
[1] 1sc9.a
0
- 0.2 0.7 1.0 0.2 - 0.7 0.4
[1] 1sck.a 0.2
-
0.1 0.5 1.2 0.4 - 0.6 0.4
[1] 1scq.a 0.1 -
0
0.4 0.9 0.2 - 0.8 0.1
[1] 1yas.a 0.1 - 0.1
0.2
0.8 0.2 - 0.5 0.5
[1] 1yb6.a 0.1 - 0.1 0.5
0.5
0.1 - 0.8 0.4
[1] 1yb7.a 0.1 - 0.1 0.4 0.5
0.1
- 0.7 0.5
[1] 3c6x.a 0.2 - 0.1 0.8 1.2 0.4
-
0.7 0.4
[1] 4yas.a 0.2 - 0.2 0.6 1.2 0.4 -
0.7
0.2
[1] 5yas.a 0.2 - 0.2 0.6 0.7 0 - 0.7
0.1
[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
1sc9.a
1sck.a
1scq.a
1yas.a
1yb6.a
1yb7.a
3c6x.a
4yas.a
5yas.a
[1] 1sc9.a
0
.03 .03 .03 .05 .04 .02 .03 .06
[1] 1sck.a .03
0
.04 .03 .07 .07 .03 .04 .07
[1] 1scq.a .03 .04
0
.06 .07 .07 .03 .01 .05
[1] 1yas.a .03 .03 .06
0
.05 .05 .05 .06 .07
[1] 1yb6.a .05 .07 .07 .05
0
.01 .05 .07 .04
[1] 1yb7.a .04 .07 .07 .05 .01
0
.06 .07 .05
[1] 3c6x.a .02 .03 .03 .05 .05 .06
0
.02 .04
[1] 4yas.a .03 .04 .01 .06 .07 .07 .02
0
.03
[1] 5yas.a .06 .07 .05 .07 .04 .05 .04 .03
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
1sc9.a
1sck.a
1scq.a
1yas.a
1yb6.a
1yb7.a
3c6x.a
4yas.a
5yas.a
[1] 1sc9.a
0
0.3 0.2 0.2 0.1 0.1 0.2 0.2 0.1
[1] 1sck.a 0.3
0
0.2 0.3 0.2 0.2 0.2 0.3 0.2
[1] 1scq.a 0.2 0.2
0
0.2 0.2 0.2 0.2 0.2 0.2
[1] 1yas.a 0.2 0.3 0.2
0
0.2 0.2 0.2 0.2 0.2
[1] 1yb6.a 0.1 0.2 0.2 0.2
0
0.1 0.1 0.2 0.1
[1] 1yb7.a 0.1 0.2 0.2 0.2 0.1
0
0.1 0.2 0.1
[1] 3c6x.a 0.2 0.2 0.2 0.2 0.1 0.1
0
0.2 0.1
[1] 4yas.a 0.2 0.3 0.2 0.2 0.2 0.2 0.2
0
0.2
[1] 5yas.a 0.1 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
1sc9.a
1sck.a
1scq.a
1yas.a
1yb6.a
1yb7.a
3c6x.a
4yas.a
5yas.a
[1] 1sc9.a
0
0.5 0.3 0.6 0.2 0.2 0.2 0.4 0.5
[1] 1sck.a 0.5
0
0.4 0.7 0.5 0.5 0.4 0.5 0.6
[1] 1scq.a 0.3 0.4
0
0.5 0.3 0.2 0.3 0.4 0.5
[1] 1yas.a 0.6 0.7 0.5
0
0.5 0.5 0.5 0.6 0.3
[1] 1yb6.a 0.2 0.5 0.3 0.5
0
0.1 0.2 0.4 0.5
[1] 1yb7.a 0.2 0.5 0.2 0.5 0.1
0
0.2 0.4 0.5
[1] 3c6x.a 0.2 0.4 0.3 0.5 0.2 0.2
0
0.3 0.5
[1] 4yas.a 0.4 0.5 0.4 0.6 0.4 0.4 0.3
0
0.6
[1] 5yas.a 0.5 0.6 0.5 0.3 0.5 0.5 0.5 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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