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CHIA_HUMAN_20_404

Acidic mammalian chitinase [Glycosyl hydrolase 18 family. Chitinase class II subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CHIA_HUMAN):R: Chitooligosaccharide binding (98:100)
R: Chitooligosaccharide binding (210, 212, 213)
27, 31, 35, 58, 69, 138, 140, 183, 267, 295, 297, 300, 302, 358, 360, 364
27, 31, 35, 58, 69, 98:100, 138, 140, 183, 210, 212, 213, 267, 295, 297, 300, 302, 358, 360, 364

Full PDB list

2ybt, 2ybu, 3fxy, 3fy1, 3rm4, 3rm8, 3rm9, 3rme

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
2
7
W
3
1
R
3
5
F
5
8
I
6
9
G
9
8
W
9
9
N
1
0
0
D
1
3
8
E
1
4
0
A
1
8
3
M
2
1
0
Y
2
1
2
D
2
1
3
Y
2
6
7
A
2
9
5
E
2
9
7
I
3
0
0
M
3
5
8
W
3
6
0
L
3
6
4
[1]2ybt.a dw029 . . . . . . . . . . . . . . . . . . . . .
[1]2ybu.a cx928 . . . . . . . . . . . . . . . . . . . . .
[1]3fxy.a none . . . . . . . . . . . . . . . . . . . . .
[1]3fy1.a na1.naa.ami44 . . . . . . . . . . . . . . . . . . . . .
[1]3fy1.b na1,naa.ami44 . . . . . . . . . . . . . . . . . . . . .
[1]3rm4.a 3rm22 . . . . . . . . . . . . . . . . . . . . .
[1]3rm8.a rm823 . . . . . . . . . . . . . . . . . . . . .
[1]3rm9.a 61316 . . . . . . . . . . . . . . . . . . . . .
[1]3rme.a rme18 . . . . . . . . . . . . . . . . . . . . .

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
2
7
W
3
1
R
3
5
F
5
8
I
6
9
G
9
8
W
9
9
N
1
0
0
D
1
3
8
E
1
4
0
A
1
8
3
M
2
1
0
Y
2
1
2
D
2
1
3
Y
2
6
7
A
2
9
5
E
2
9
7
I
3
0
0
A
3
0
2
M
3
5
8
W
3
6
0
L
3
6
4
[1]2ybt.a . . . . . . . . . . . . . . . . . . . . . .
[1]2ybu.a . . . . . . . . * . . . . . . . * . . . . .
[1]3fxy.a . . . . . . . . . . . . . . . . * . . . . .
[1]3fy1.a . . . . . . . . * . . . . . . . * . . . . .
[1]3fy1.b . . . . . . . . * . . . . . . . * . . . . .
[1]3rm4.a . . . . . . . . . . . . . . . . . . . . . .
[1]3rm8.a . . . . . . * . . . . . . . . . . . . . . .
[1]3rm9.a . . . . . . . . * . . . . . . . . . . . . .
[1]3rme.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
2ybt.a:dw0
2ybu.a:cx9
3fxy.a is apo
3fy1.a:na1.naa.ami
3fy1.b:na1,naa.ami
3rm4.a:3rm
3rm8.a:rm8
3rm9.a:613
3rme.a:rme
[1] 2ybt.a
0
0 - 1.6 1.5 0.2 0.1 0 0
[1] 2ybu.a 1.1
0.1
- 1.6 1.6 0.4 0.5 0 0.5
[1] 3fxy.a 0.4 0.3
-
0.8 0.8 1.3 1.4 0.7 0.5
[1] 3fy1.a 1.0 0.1 -
0
0 1.2 1.0 0.9 0.3
[1] 3fy1.b 1.1 0.2 - 0
0
1.2 0.7 0.9 0.3
[1] 3rm4.a 0.4 0.1 - 0.5 0.6
0
0.2 0.1 0.3
[1] 3rm8.a 4.1 3.9 - 4.8 4.8 0.1
0
0 3.5
[1] 3rm9.a 1.1 0 - 0.9 0.9 0.4 0.4
0
0.4
[1] 3rme.a 0.2 0 - 1.3 1.3 0.3 0.1 0
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
2ybt.a
2ybu.a
3fxy.a
3fy1.a
3fy1.b
3rm4.a
3rm8.a
3rm9.a
3rme.a
[1] 2ybt.a
0
.06 .06 .07 .08 .08 .22 .05 .04
[1] 2ybu.a .06
0
.07 .03 .03 .10 .22 .03 .06
[1] 3fxy.a .06 .07
0
.08 .07 .10 .25 .09 .07
[1] 3fy1.a .07 .03 .08
0
.01 .10 .24 .03 .07
[1] 3fy1.b .08 .03 .07 .01
0
.09 .24 .04 .07
[1] 3rm4.a .08 .10 .10 .10 .09
0
.24 .10 .08
[1] 3rm8.a .22 .22 .25 .24 .24 .24
0
.23 .21
[1] 3rm9.a .05 .03 .09 .03 .04 .10 .23
0
.06
[1] 3rme.a .04 .06 .07 .07 .07 .08 .21 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2ybt.a
2ybu.a
3fxy.a
3fy1.a
3fy1.b
3rm4.a
3rm8.a
3rm9.a
3rme.a
[1] 2ybt.a
0
0.1 0.3 0.3 0.3 0.3 0.3 0.2 0.2
[1] 2ybu.a 0.1
0
0.3 0.3 0.3 0.2 0.3 0.3 0.2
[1] 3fxy.a 0.3 0.3
0
0.4 0.4 0.4 0.2 0.2 0.3
[1] 3fy1.a 0.3 0.3 0.4
0
0.1 0.3 0.4 0.3 0.3
[1] 3fy1.b 0.3 0.3 0.4 0.1
0
0.3 0.4 0.3 0.3
[1] 3rm4.a 0.3 0.2 0.4 0.3 0.3
0
0.4 0.3 0.3
[1] 3rm8.a 0.3 0.3 0.2 0.4 0.4 0.4
0
0.2 0.3
[1] 3rm9.a 0.2 0.3 0.2 0.3 0.3 0.3 0.2
0
0.2
[1] 3rme.a 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.2
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
2ybt.a
2ybu.a
3fxy.a
3fy1.a
3fy1.b
3rm4.a
3rm8.a
3rm9.a
3rme.a
[1] 2ybt.a
0
0.5 0.9 1.0 1.0 0.8 1.6 0.8 0.8
[1] 2ybu.a 0.5
0
0.9 0.8 0.8 0.8 1.6 0.7 0.8
[1] 3fxy.a 0.9 0.9
0
0.7 0.7 0.8 1.4 0.7 0.7
[1] 3fy1.a 1.0 0.8 0.7
0
0.1 0.8 1.6 0.5 0.7
[1] 3fy1.b 1.0 0.8 0.7 0.1
0
0.7 1.6 0.5 0.7
[1] 3rm4.a 0.8 0.8 0.8 0.8 0.7
0
1.5 0.7 0.6
[1] 3rm8.a 1.6 1.6 1.4 1.6 1.6 1.5
0
1.5 1.5
[1] 3rm9.a 0.8 0.7 0.7 0.5 0.5 0.7 1.5
0
0.5
[1] 3rme.a 0.8 0.8 0.7 0.7 0.7 0.6 1.5 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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