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CH3L1_BOVIN_22_383

Chitinase-3-like protein 1 [Glycosyl hydrolase 18 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CH3L1_BOVIN):R: Chitooligosaccharide binding (70, 71)
R: Chitooligosaccharide binding (98:100)
R: Chitooligosaccharide binding (204, 206, 207)
27, 29, 31, 34, 35, 58, 69, 138, 140, 141, 177, 211, 212, 261, 263, 281, 288:291, 293, 350, 352, 356
27, 29, 31, 34, 35, 58, 69:71, 98:100, 138, 140, 141, 177, 204, 206, 207, 211, 212, 261, 263, 281, 288:291, 293, 350, 352, 356

Full PDB list

1ljy, 1owq, 1sr0, 1syt, 1tfv, 1xhg, 1xrv, 1zb5, 1zbc, 1zbk, 1zbv, 1zbw, 1zl1, 1zu8, 2aos, 2b31, 2dpe, 2dsu, 2dsv, 2dsw, 2dsz, 2dt0, 2dt1, 2dt2, 2dt3, 2esc, 2fdm, 2g41, 2g8z, 2o92, 2o9o, 2olh, 2pi6, 2qf8, 4mav, 4ml4, 4mpk, 4mtv, 4nsb, 4q7n, 4s06, 5wsi, 5wsm, 5yar (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
2
7
W
3
1
Y
3
4
R
3
5
F
5
8
W
6
9
E
7
0
W
7
1
W
9
9
N
1
0
0
A
1
3
8
L
1
4
0
Y
1
4
1
L
2
0
4
Y
2
0
6
D
2
0
7
W
2
1
2
F
2
6
1
R
2
6
3
T
2
8
8
K
2
8
9
E
2
9
0
I
2
9
3
W
3
5
2
L
3
5
6
[1]1owq.a none . . . . . . . . . . . . . . . . . . . . . . T . .
[1]1tfv.a none . . . . . . . . . . . . W . . . . . . . . W . . .
[1]1zbv.a WPW36 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zl1.a WHW38 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zu8.a nag.ndg.ndg42 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2b31.a nag.ndg.nag.nag.nag70 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2esc.a none . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2olh.a cbi23 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2pi6.a none . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4mav.a rib10 . . . . . . . . . . . . W . . . . . . . . W . . .
[1]4ml4.a pye6 . . . . . . . . . . . . W . . . . . . . . W . . .
[1]4nsb.a ain13 . . . . . . . . . . . . W . . . . . . . . W . . .
[1]4q7n.a 2zo9 . . . . . . . . . . . . W . . . . . . . . W . . .
[1]4s06.a none . . . . . . . . . . . . . . . . . . K . . . . . .
[1]5yar.a rib10 . . . . . . . . . . . . . . . . . . K . . . . . .

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
T
2
9
W
3
1
Y
3
4
R
3
5
F
5
8
W
6
9
E
7
0
W
7
1
G
9
8
W
9
9
N
1
0
0
A
1
3
8
L
1
4
0
Y
1
4
1
A
1
7
7
L
2
0
4
Y
2
0
6
D
2
0
7
A
2
1
1
W
2
1
2
F
2
6
1
R
2
6
3
P
2
8
1
T
2
8
8
K
2
8
9
E
2
9
0
K
2
9
1
I
2
9
3
M
3
5
0
W
3
5
2
L
3
5
6
[1]1owq.a . . . . . . . . . . * . . . . . . . . G . . . . . . * . T . . .
[1]1tfv.a . . . . . . . . . . * . . . W . . . . . . . . . . . W . . . . .
[1]1zbv.a . . . . . . . . . . * . . . . . . . . . . . . . . . * . . . . .
[1]1zl1.a . . . . . . . . . . * . . . . . . . . . . . . . . . * . . . . .
[1]1zu8.a . . . . . . . . . . * . . . . . . . . . . . . . . . * . . . . .
[1]2b31.a . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]2esc.a . . . . . . . . . . * . . . . . . . . G . . . . . . * . . . . .
[1]2olh.a . . . . . . . . . . * * . . . . . . . . . . . . . . * . . . . .
[1]2pi6.a . . . . . . . . . . * * . . . . . . . . . . . . . . . . . . . .
[1]4mav.a . . . . . . . . . . * * . . W . . . . . . . . . . . W . . . . .
[1]4ml4.a . . . . . . . . . . * * . . W . . . . . . . . . . . W . . . . .
[1]4nsb.a . . . . . . . . . . * * . . W . . . . . . . . . . . W . . . . .
[1]4q7n.a . . . . . . . . . . * * . . W . . . . . . . . . . . W . . . . .
[1]4s06.a . . . . . . . . . . * * . . . . . . . . . . K . . . . . . . . .
[1]5yar.a . . . . * . . . . . * * . . . . . . . . . . K . . . . . . . . .

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
1owq.a is apo
1tfv.a is apo
1zbv.a:WPW
1zl1.a:WHW
1zu8.a:nag.ndg.ndg
2b31.a:nag.ndg.nag.nag.nag
2esc.a is apo
2olh.a:cbi
2pi6.a is apo
4mav.a:rib
4ml4.a:pye
4nsb.a:ain
4q7n.a:2zo
4s06.a is apo
5yar.a:rib
[1] 1owq.a
-
- 0 0 0.7 3.1 - 0.4 - 2.3 1.9 2.1 1.0 - 2.6
[1] 1tfv.a -
-
3.9 0 2.5 2.7 - 2.6 - 0 0.4 3.8 4.0 - 0.2
[1] 1zbv.a - -
0
0 0.7 3.8 - 0.2 - 2.9 2.3 1.4 0.5 - 3.0
[1] 1zl1.a - - 0
0
0.7 3.5 - 0.3 - 2.5 2.3 1.7 0.7 - 2.6
[1] 1zu8.a - - 0 0
0.5
2.8 - 0.4 - 3.2 2.5 1.7 0.9 - 2.8
[1] 2b31.a - - 0.2 0 0.2
0
- 0.5 - 0.3 0.2 1.8 0.7 - 0
[1] 2esc.a - - 0 0 0.4 3.1
-
0.5 - 2.0 2.3 2.3 1.0 - 2.8
[1] 2olh.a - - 0.1 0 1.4 4.5 -
0.1
- 3.0 2.6 1.7 1.0 - 2.9
[1] 2pi6.a - - 0.1 0 3.8 5.0 - 3.1
-
0.1 0.2 0.6 0 - 0.4
[1] 4mav.a - - 0.3 0 3.6 4.8 - 2.8 -
0
0.1 0.5 0.1 - 0.6
[1] 4ml4.a - - 0.9 0.1 3.4 5.0 - 2.3 - 0.1
0.2
0.5 0.1 - 0.9
[1] 4nsb.a - - 0.5 0.1 3.5 4.6 - 2.5 - 0 0.1
0.2
0 - 0.6
[1] 4q7n.a - - 1.6 0 3.6 5.5 - 2.5 - 0.2 0.2 0.9
0.2
- 0.9
[1] 4s06.a - - 0.1 0 3.9 4.9 - 2.8 - 0 0.2 0.5 0.1
-
0.6
[1] 5yar.a - - 0 0 4.0 4.6 - 3.2 - 0.1 0.2 0.8 0.1 -
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
1owq.a
1tfv.a
1zbv.a
1zl1.a
1zu8.a
2b31.a
2esc.a
2olh.a
2pi6.a
4mav.a
4ml4.a
4nsb.a
4q7n.a
4s06.a
5yar.a
[1] 1owq.a
0
.16 .06 .04 .03 .12 .01 .06 .11 .09 .08 .09 .08 .10 .09
[1] 1tfv.a .16
0
.16 .16 .16 .28 .16 .17 .18 .19 .18 .17 .17 .20 .20
[1] 1zbv.a .06 .16
0
.05 .04 .15 .06 .05 .08 .08 .06 .05 .10 .08 .08
[1] 1zl1.a .04 .16 .05
0
.03 .12 .04 .04 .09 .08 .07 .07 .08 .09 .08
[1] 1zu8.a .03 .16 .04 .03
0
.12 .04 .04 .09 .08 .07 .08 .08 .09 .08
[1] 2b31.a .12 .28 .15 .12 .12
0
.12 .15 .21 .19 .18 .19 .19 .20 .19
[1] 2esc.a .01 .16 .06 .04 .04 .12
0
.07 .11 .10 .09 .10 .09 .11 .10
[1] 2olh.a .06 .17 .05 .04 .04 .15 .07
0
.06 .05 .03 .05 .05 .05 .06
[1] 2pi6.a .11 .18 .08 .09 .09 .21 .11 .06
0
.03 .05 .04 .08 .02 .02
[1] 4mav.a .09 .19 .08 .08 .08 .19 .10 .05 .03
0
.03 .02 .07 .01 .04
[1] 4ml4.a .08 .18 .06 .07 .07 .18 .09 .03 .05 .03
0
.03 .06 .04 .06
[1] 4nsb.a .09 .17 .05 .07 .08 .19 .10 .05 .04 .02 .03
0
.08 .04 .05
[1] 4q7n.a .08 .17 .10 .08 .08 .19 .09 .05 .08 .07 .06 .08
0
.07 .09
[1] 4s06.a .10 .20 .08 .09 .09 .20 .11 .05 .02 .01 .04 .04 .07
0
.04
[1] 5yar.a .09 .20 .08 .08 .08 .19 .10 .06 .02 .04 .06 .05 .09 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1owq.a
1tfv.a
1zbv.a
1zl1.a
1zu8.a
2b31.a
2esc.a
2olh.a
2pi6.a
4mav.a
4ml4.a
4nsb.a
4q7n.a
4s06.a
5yar.a
[1] 1owq.a
0
0.8 0.8 0.8 0.7 0.8 0.4 0.7 0.8 0.5 0.6 0.8 0.5 0.5 0.4
[1] 1tfv.a 0.8
0
1.1 1.0 1.0 1.0 0.9 1.0 1.2 1.0 1.0 1.1 1.0 1.0 0.9
[1] 1zbv.a 0.8 1.1
0
0.6 0.3 0.6 0.9 0.4 0.7 0.9 0.8 0.8 1.0 1.0 1.0
[1] 1zl1.a 0.8 1.0 0.6
0
0.5 0.6 0.8 0.5 0.8 0.9 0.8 0.9 1.0 1.0 1.0
[1] 1zu8.a 0.7 1.0 0.3 0.5
0
0.4 0.8 0.3 0.7 0.9 0.7 0.8 1.0 1.0 0.9
[1] 2b31.a 0.8 1.0 0.6 0.6 0.4
0
0.9 0.5 0.9 0.9 0.8 0.9 1.0 1.0 1.0
[1] 2esc.a 0.4 0.9 0.9 0.8 0.8 0.9
0
0.8 0.8 0.4 0.5 0.8 0.3 0.3 0.3
[1] 2olh.a 0.7 1.0 0.4 0.5 0.3 0.5 0.8
0
0.7 0.8 0.7 0.8 0.9 0.9 0.9
[1] 2pi6.a 0.8 1.2 0.7 0.8 0.7 0.9 0.8 0.7
0
0.8 0.6 0.5 0.8 0.8 0.8
[1] 4mav.a 0.5 1.0 0.9 0.9 0.9 0.9 0.4 0.8 0.8
0
0.4 0.6 0.4 0.3 0.3
[1] 4ml4.a 0.6 1.0 0.8 0.8 0.7 0.8 0.5 0.7 0.6 0.4
0
0.5 0.5 0.4 0.4
[1] 4nsb.a 0.8 1.1 0.8 0.9 0.8 0.9 0.8 0.8 0.5 0.6 0.5
0
0.8 0.8 0.7
[1] 4q7n.a 0.5 1.0 1.0 1.0 1.0 1.0 0.3 0.9 0.8 0.4 0.5 0.8
0
0.1 0.2
[1] 4s06.a 0.5 1.0 1.0 1.0 1.0 1.0 0.3 0.9 0.8 0.3 0.4 0.8 0.1
0
0.1
[1] 5yar.a 0.4 0.9 1.0 1.0 0.9 1.0 0.3 0.9 0.8 0.3 0.4 0.7 0.2 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1owq.a
1tfv.a
1zbv.a
1zl1.a
1zu8.a
2b31.a
2esc.a
2olh.a
2pi6.a
4mav.a
4ml4.a
4nsb.a
4q7n.a
4s06.a
5yar.a
[1] 1owq.a
0
2.2 1.2 1.6 1.1 1.6 0.3 1.3 1.6 1.1 1.1 1.3 0.9 1.1 1.1
[1] 1tfv.a 2.2
0
2.3 1.7 2.3 2.4 2.2 2.3 2.4 2.3 2.3 2.5 2.2 2.2 2.1
[1] 1zbv.a 1.2 2.3
0
2.0 0.4 1.3 1.3 0.8 1.2 1.3 1.1 1.2 1.7 1.7 1.4
[1] 1zl1.a 1.6 1.7 2.0
0
2.0 2.3 1.6 2.0 2.3 1.9 1.9 2.2 1.7 1.8 2.0
[1] 1zu8.a 1.1 2.3 0.4 2.0
0
1.1 1.2 0.8 1.3 1.3 1.1 1.1 1.6 1.7 1.4
[1] 2b31.a 1.6 2.4 1.3 2.3 1.1
0
1.6 1.2 1.6 1.6 1.5 1.5 2.0 1.9 1.6
[1] 2esc.a 0.3 2.2 1.3 1.6 1.2 1.6
0
1.4 1.6 1.1 1.2 1.4 0.9 1.1 1.1
[1] 2olh.a 1.3 2.3 0.8 2.0 0.8 1.2 1.4
0
1.2 1.3 1.2 1.2 1.7 1.8 1.5
[1] 2pi6.a 1.6 2.4 1.2 2.3 1.3 1.6 1.6 1.2
0
1.1 0.9 0.8 1.7 1.6 1.1
[1] 4mav.a 1.1 2.3 1.3 1.9 1.3 1.6 1.1 1.3 1.1
0
0.6 0.7 1.2 1.0 0.5
[1] 4ml4.a 1.1 2.3 1.1 1.9 1.1 1.5 1.2 1.2 0.9 0.6
0
0.7 1.3 1.1 0.7
[1] 4nsb.a 1.3 2.5 1.2 2.2 1.1 1.5 1.4 1.2 0.8 0.7 0.7
0
1.6 1.4 0.9
[1] 4q7n.a 0.9 2.2 1.7 1.7 1.6 2.0 0.9 1.7 1.7 1.2 1.3 1.6
0
0.6 1.0
[1] 4s06.a 1.1 2.2 1.7 1.8 1.7 1.9 1.1 1.8 1.6 1.0 1.1 1.4 0.6
0
0.8
[1] 5yar.a 1.1 2.1 1.4 2.0 1.4 1.6 1.1 1.5 1.1 0.5 0.7 0.9 1.0 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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