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CHIA_SERMA_19_563

Chitinase A [Glycosyl hydrolase 18 family. Chitinase class II subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CHIA_SERMA):R: Catalytic (163, 167, 172, 191, 204, 207, 210, 229, 274:277, 313, 315, 362, 388, 390, 391, 444, 446, 473, 476, 537, 539, 540)163, 167, 172, 191, 204, 207, 210, 229, 274:277, 313, 315, 362, 388, 390, 391, 444, 446, 473, 476, 537, 539, 540

Full PDB list

1ctn, 1edq, 1ehn, 1eib, 1ffq, 1ffr, 1k9t, 1nh6, 1rd6, 1x6l, 1x6n, 2wk2, 2wly, 2wlz, 2wm0 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
1
6
3
W
1
6
7
R
1
7
2
F
1
9
1
L
2
0
4
I
2
0
7
S
2
1
0
H
2
2
9
W
2
7
5
T
2
7
6
L
2
7
7
D
3
1
3
E
3
1
5
A
3
6
2
M
3
8
8
Y
3
9
0
D
3
9
1
Y
4
4
4
R
4
4
6
K
4
7
3
I
4
7
6
F
5
3
7
W
5
3
9
E
5
4
0
[1]1edq.a none . . . . . . . . . . . . . . . . . . . E . . . .
[1]1ehn.a none . . . . . . . . . . . . Q . . . . . . E . . . .
[1]1eib.a none . . . . . . . . . . . A . . . . . . . E . . . .
[1]1ffq.a naa.naa.ami43 . . . . . . . . . . . . . . . . . . . E . . . .
[1]1ffr.a none . . . . . . . . . . . . . . . F . . . E . . . .
[1]1k9t.a none . . . . . . . . . . . . . . . . A . . E . . . .
[1]1nh6.a none . . . . . . . . . . . . L . . . . . . E . . . .
[1]1x6l.a none . A . . . . . . . . . . . . . . . . . E . . . .
[1]1x6n.a ao343 . A . . . . . . . . . . . . . . . . . E . . . .
[1]2wk2.a sn5.sn5.ngt42 . . . . . . . . . . . . . . . . . . . E . . . .
[1]2wly.a dio,sn5.ngt34 . . . . . . . . . . . . . . . . . . . E . . . .
[1]2wlz.a dio6 . . . . . . . . . . . . . . . . . . . E . . . .

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
Y
1
6
3
W
1
6
7
R
1
7
2
F
1
9
1
L
2
0
4
I
2
0
7
S
2
1
0
H
2
2
9
G
2
7
4
W
2
7
5
T
2
7
6
L
2
7
7
D
3
1
3
E
3
1
5
A
3
6
2
M
3
8
8
Y
3
9
0
D
3
9
1
Y
4
4
4
R
4
4
6
K
4
7
3
I
4
7
6
F
5
3
7
W
5
3
9
E
5
4
0
[1]1edq.a . . . . . . . . . . . . . . . . . . . . E . . . .
[1]1ehn.a . . . . . . . . . . . . . Q . . . . . . E . . . .
[1]1eib.a . . . . . . . . . . . . A . . . . . . . E . . . .
[1]1ffq.a . . . . . . . . . . . . . . . . . . . . E . . . .
[1]1ffr.a . . . . . . . . . . . . . . . . F . . . E . . . .
[1]1k9t.a . . . . . . . . . . . . . . . . . A . . E . . . .
[1]1nh6.a . . . . . . . . . . . . . L . . . . . . E . . . .
[1]1x6l.a . A . . . . . . . . . . . . . . . . . . E . . . .
[1]1x6n.a . A . . . . . . . . . . . . . . . . . . E . . . .
[1]2wk2.a . . . . . . . . . . . . . . . . . . . . E . . . .
[1]2wly.a . . . . . . . . . . . . . . . . . . . . E . . . .
[1]2wlz.a . . . . . . . . . . . . . . . . . . . . E . . . .

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
1edq.a is apo
1ehn.a is apo
1eib.a is apo
1ffq.a:naa.naa.ami
1ffr.a is apo
1k9t.a is apo
1nh6.a is apo
1x6l.a is apo
1x6n.a:ao3
2wk2.a:sn5.sn5.ngt
2wly.a:dio,sn5.ngt
2wlz.a:dio
[1] 1edq.a
-
- - 0.9 - - - - 1.4 0.4 0.5 0
[1] 1ehn.a -
-
- 0.6 - - - - 0.8 0.2 0.4 0
[1] 1eib.a - -
-
0.8 - - - - 0.7 0.4 0.4 0
[1] 1ffq.a - - -
0.1
- - - - 0.1 0.3 0.4 0
[1] 1ffr.a - - - 0.5
-
- - - 0.7 0.5 0.5 0
[1] 1k9t.a - - - 0.5 -
-
- - 0.5 0.6 0.7 0
[1] 1nh6.a - - - 0.7 - -
-
- 0.6 0.3 0.2 0.1
[1] 1x6l.a - - - 1.2 - - -
-
1.2 0.8 1.0 0.1
[1] 1x6n.a - - - 0 - - - -
0
0.3 0.3 0
[1] 2wk2.a - - - 0.9 - - - - 1.0
0.1
0.1 0
[1] 2wly.a - - - 0.9 - - - - 0.9 0.1
0.1
0
[1] 2wlz.a - - - 1.0 - - - - 0.8 0.1 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
1edq.a
1ehn.a
1eib.a
1ffq.a
1ffr.a
1k9t.a
1nh6.a
1x6l.a
1x6n.a
2wk2.a
2wly.a
2wlz.a
[1] 1edq.a
0
.06 .05 .06 .04 .04 .09 .06 .06 .05 .04 .04
[1] 1ehn.a .06
0
.03 .04 .05 .04 .03 .04 .05 .01 .03 .04
[1] 1eib.a .05 .03
0
.04 .04 .02 .04 .05 .04 .03 .04 .05
[1] 1ffq.a .06 .04 .04
0
.04 .04 .05 .05 .01 .05 .05 .05
[1] 1ffr.a .04 .05 .04 .04
0
.02 .08 .04 .03 .06 .04 .05
[1] 1k9t.a .04 .04 .02 .04 .02
0
.07 .05 .03 .05 .04 .04
[1] 1nh6.a .09 .03 .04 .05 .08 .07
0
.06 .05 .04 .06 .07
[1] 1x6l.a .06 .04 .05 .05 .04 .05 .06
0
.06 .05 .06 .04
[1] 1x6n.a .06 .05 .04 .01 .03 .03 .05 .06
0
.06 .05 .06
[1] 2wk2.a .05 .01 .03 .05 .06 .05 .04 .05 .06
0
.02 .02
[1] 2wly.a .04 .03 .04 .05 .04 .04 .06 .06 .05 .02
0
.01
[1] 2wlz.a .04 .04 .05 .05 .05 .04 .07 .04 .06 .02 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1edq.a
1ehn.a
1eib.a
1ffq.a
1ffr.a
1k9t.a
1nh6.a
1x6l.a
1x6n.a
2wk2.a
2wly.a
2wlz.a
[1] 1edq.a
0
0.2 0.2 0.3 0.2 0.2 0.4 0.5 0.5 0.2 0.3 0.2
[1] 1ehn.a 0.2
0
0.2 0.2 0.2 0.2 0.3 0.5 0.5 0.2 0.3 0.2
[1] 1eib.a 0.2 0.2
0
0.3 0.1 0.2 0.4 0.5 0.5 0.2 0.2 0.2
[1] 1ffq.a 0.3 0.2 0.3
0
0.3 0.3 0.3 0.5 0.4 0.3 0.4 0.3
[1] 1ffr.a 0.2 0.2 0.1 0.3
0
0.2 0.4 0.5 0.5 0.2 0.2 0.2
[1] 1k9t.a 0.2 0.2 0.2 0.3 0.2
0
0.4 0.5 0.5 0.2 0.2 0.2
[1] 1nh6.a 0.4 0.3 0.4 0.3 0.4 0.4
0
0.5 0.5 0.4 0.4 0.4
[1] 1x6l.a 0.5 0.5 0.5 0.5 0.5 0.5 0.5
0
0.3 0.5 0.5 0.5
[1] 1x6n.a 0.5 0.5 0.5 0.4 0.5 0.5 0.5 0.3
0
0.5 0.5 0.5
[1] 2wk2.a 0.2 0.2 0.2 0.3 0.2 0.2 0.4 0.5 0.5
0
0.2 0.1
[1] 2wly.a 0.3 0.3 0.2 0.4 0.2 0.2 0.4 0.5 0.5 0.2
0
0.1
[1] 2wlz.a 0.2 0.2 0.2 0.3 0.2 0.2 0.4 0.5 0.5 0.1 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1edq.a
1ehn.a
1eib.a
1ffq.a
1ffr.a
1k9t.a
1nh6.a
1x6l.a
1x6n.a
2wk2.a
2wly.a
2wlz.a
[1] 1edq.a
0
0.5 0.3 0.6 0.4 0.5 0.5 0.7 0.6 0.3 0.3 0.2
[1] 1ehn.a 0.5
0
0.4 0.7 0.6 0.6 0.5 0.8 0.7 0.5 0.5 0.5
[1] 1eib.a 0.3 0.4
0
0.4 0.2 0.3 0.4 0.6 0.5 0.3 0.3 0.3
[1] 1ffq.a 0.6 0.7 0.4
0
0.4 0.5 0.7 0.7 0.4 0.6 0.6 0.6
[1] 1ffr.a 0.4 0.6 0.2 0.4
0
0.4 0.6 0.6 0.5 0.4 0.5 0.4
[1] 1k9t.a 0.5 0.6 0.3 0.5 0.4
0
0.7 0.7 0.5 0.5 0.6 0.5
[1] 1nh6.a 0.5 0.5 0.4 0.7 0.6 0.7
0
0.7 0.7 0.5 0.5 0.5
[1] 1x6l.a 0.7 0.8 0.6 0.7 0.6 0.7 0.7
0
0.6 0.7 0.7 0.7
[1] 1x6n.a 0.6 0.7 0.5 0.4 0.5 0.5 0.7 0.6
0
0.6 0.7 0.6
[1] 2wk2.a 0.3 0.5 0.3 0.6 0.4 0.5 0.5 0.7 0.6
0
0.2 0.2
[1] 2wly.a 0.3 0.5 0.3 0.6 0.5 0.6 0.5 0.7 0.7 0.2
0
0.2
[1] 2wlz.a 0.2 0.5 0.3 0.6 0.4 0.5 0.5 0.7 0.6 0.2 0.2
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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