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CHIB1_ASPFM_39_433

Endochitinase B1 [Glycosyl hydrolase 18 family. Chitinase class V subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CHIB1_ASPFM):R: Inhibitor binding (175, 177)
48, 52, 57, 76, 136:139, 178, 217, 243, 245, 246, 248:252, 299, 301, 321, 322, 325, 382, 384
48, 52, 57, 76, 136:139, 175, 177, 178, 217, 243, 245, 246, 248:252, 299, 301, 321, 322, 325, 382, 384

Full PDB list

1w9p, 1w9u, 1w9v, 1wno, 2a3a, 2a3b, 2a3c, 2a3e, 2iuz, 3ch9, 3chc, 3chd, 3che, 3chf (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
4
8
W
5
2
R
5
7
F
7
6
G
1
3
6
W
1
3
7
T
1
3
8
Y
1
3
9
D
1
7
5
E
1
7
7
Y
1
7
8
A
2
1
7
M
2
4
3
Y
2
4
5
D
2
4
6
A
2
4
8
G
2
4
9
S
2
5
0
F
2
5
1
Y
2
9
9
R
3
0
1
E
3
2
2
V
3
2
5
M
3
8
2
W
3
8
4
[1]1w9p.b none . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1w9u.a 0ar.dprDHun148 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1w9v.b vr0.mea.ias.ias.dal48 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2a3a.b tep,tep,tep,tep52 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2a3b.b cff,cff,cff42 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2a3c.a pnx,pnx40 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2a3e.a naa.naa.ami43 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iuz.b d1h28 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ch9.b xrg9 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3chc.b zrg20 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3chd.b wrg31 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3che.b ace.vr0.meaD39 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3chf.b ace.dal.vr0.meaD44 . . . . . . . . . . . . . . . . . . . . . . . . .

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
4
8
W
5
2
R
5
7
F
7
6
G
1
3
6
W
1
3
7
T
1
3
8
Y
1
3
9
D
1
7
5
E
1
7
7
Y
1
7
8
A
2
1
7
M
2
4
3
Y
2
4
5
D
2
4
6
A
2
4
8
G
2
4
9
S
2
5
0
F
2
5
1
S
2
5
2
Y
2
9
9
R
3
0
1
W
3
2
1
E
3
2
2
V
3
2
5
M
3
8
2
W
3
8
4
[1]1w9p.b . . . . . * . . * . . . . . . . . . * . . . . * . . .
[1]1w9u.a . . . . . * . . . . . . . . . . . . * . . . . . . . .
[1]1w9v.b . . . . . * . . * . . . . . . . . . * . . . . * . . *
[1]2a3a.b . . . . . * . . . . . . . . . . . . * . . . . * . . .
[1]2a3b.b . . . . . * . . . . . . . . . . . . * . . . . * . . .
[1]2a3c.a . . . . . * . . . . . . . . . . . . * . . . . * . . .
[1]2a3e.a . . . . . * . . * . . . . . . . . . * . . . . * . . .
[1]2iuz.b . . . . . * . . . . . . . . . . . . * . . . . * . . .
[1]3ch9.b . . . . . * . . * . . . . . . . . . * . . . . * . . .
[1]3chc.b . . . . . * . . * . . . . . . . . . * . . . . * . . .
[1]3chd.b . . . . . * . . * . . . . . . . . . * . . . . * . . .
[1]3che.b . . . . . * . . * . . . . . . . . . * . . . . * . . .
[1]3chf.b . . . . . * . . * . . . . . . . . . * . . . . * . . .

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
1w9p.b is apo
1w9u.a:0ar.dprDHun1
1w9v.b:vr0.mea.ias.ias.dal
2a3a.b:tep
2a3b.b:cff
2a3c.a:pnx
2a3e.a:naa.naa.ami
2iuz.b:d1h
3ch9.b:xrg
3chc.b:zrg
3chd.b:wrg
3che.b:ace.vr0.meaD
3chf.b:ace.dal.vr0.meaD
[1] 1w9p.b
-
2.0 2.7 1.9 2.6 8.3 3.8 3.2 0.1 0.3 0.7 1.8 2.6
[1] 1w9u.a -
0
0.7 2.0 3.9 7.3 1.2 0.1 0.2 0.1 0.6 0.8 0.7
[1] 1w9v.b - 1.0
0
2.3 5.1 8.3 1.7 0.6 0 0 0.1 0 0
[1] 2a3a.b - 5.6 3.9
0.4
0.2 4.3 2.3 0.2 2.6 3.8 5.1 4.1 4.0
[1] 2a3b.b - 6.0 4.6 0.6
0.1
4.1 1.7 0 2.5 4.0 5.2 4.5 4.8
[1] 2a3c.a - 5.6 4.8 1.6 0.6
0
1.7 0 2.8 4.1 5.0 5.3 4.8
[1] 2a3e.a - 1.8 0.4 1.5 4.5 8.6
0.1
0 0.1 0.1 0.3 0.1 0.5
[1] 2iuz.b - 6.0 4.5 0.9 0.1 3.9 1.8
0
2.5 4.1 5.5 4.4 4.5
[1] 3ch9.b - 2.0 1.3 3.3 5.4 8.7 0.5 0
0
0.1 0.8 1.3 1.3
[1] 3chc.b - 2.9 1.8 2.8 3.9 8.5 4.0 3.6 0
0
0.7 0.7 1.4
[1] 3chd.b - 1.6 1.7 2.6 3.6 8.1 4.6 3.4 0 0
0.1
0.5 1.6
[1] 3che.b - 1.7 0.3 1.1 4.2 7.6 0.6 0.1 0 0.1 0.4
0
0
[1] 3chf.b - 2.0 0.4 1.2 4.1 8.0 0.5 0.1 0 0.2 0.8 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
1w9p.b
1w9u.a
1w9v.b
2a3a.b
2a3b.b
2a3c.a
2a3e.a
2iuz.b
3ch9.b
3chc.b
3chd.b
3che.b
3chf.b
[1] 1w9p.b
0
.11 .10 .09 .12 .22 .07 .12 .07 .03 .08 .02 .03
[1] 1w9u.a .11
0
.12 .14 .16 .25 .15 .16 .15 .11 .08 .11 .13
[1] 1w9v.b .10 .12
0
.15 .19 .26 .14 .19 .15 .11 .07 .09 .10
[1] 2a3a.b .09 .14 .15
0
.04 .13 .09 .04 .08 .07 .10 .09 .11
[1] 2a3b.b .12 .16 .19 .04
0
.13 .09 0 .06 .10 .12 .11 .12
[1] 2a3c.a .22 .25 .26 .13 .13
0
.20 .13 .19 .20 .20 .20 .23
[1] 2a3e.a .07 .15 .14 .09 .09 .20
0
.10 .04 .05 .07 .06 .07
[1] 2iuz.b .12 .16 .19 .04 0 .13 .10
0
.07 .11 .12 .12 .13
[1] 3ch9.b .07 .15 .15 .08 .06 .19 .04 .07
0
.05 .08 .07 .07
[1] 3chc.b .03 .11 .11 .07 .10 .20 .05 .11 .05
0
.05 .03 .05
[1] 3chd.b .08 .08 .07 .10 .12 .20 .07 .12 .08 .05
0
.06 .09
[1] 3che.b .02 .11 .09 .09 .11 .20 .06 .12 .07 .03 .06
0
.03
[1] 3chf.b .03 .13 .10 .11 .12 .23 .07 .13 .07 .05 .09 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1w9p.b
1w9u.a
1w9v.b
2a3a.b
2a3b.b
2a3c.a
2a3e.a
2iuz.b
3ch9.b
3chc.b
3chd.b
3che.b
3chf.b
[1] 1w9p.b
0
0.3 0.2 0.2 0.2 0.3 0.3 0.2 0.2 0.2 0.2 0.2 0.2
[1] 1w9u.a 0.3
0
0.3 0.3 0.3 0.2 0.3 0.3 0.2 0.2 0.2 0.3 0.3
[1] 1w9v.b 0.2 0.3
0
0.2 0.2 0.3 0.2 0.2 0.2 0.2 0.2 0.1 0.1
[1] 2a3a.b 0.2 0.3 0.2
0
0.1 0.2 0.3 0.1 0.2 0.2 0.2 0.2 0.2
[1] 2a3b.b 0.2 0.3 0.2 0.1
0
0.2 0.3 0.1 0.2 0.2 0.2 0.2 0.2
[1] 2a3c.a 0.3 0.2 0.3 0.2 0.2
0
0.3 0.2 0.2 0.2 0.2 0.2 0.3
[1] 2a3e.a 0.3 0.3 0.2 0.3 0.3 0.3
0
0.3 0.2 0.3 0.2 0.2 0.2
[1] 2iuz.b 0.2 0.3 0.2 0.1 0.1 0.2 0.3
0
0.2 0.2 0.2 0.2 0.2
[1] 3ch9.b 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
0
0.1 0.1 0.1 0.1
[1] 3chc.b 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.2 0.1
0
0.1 0.1 0.1
[1] 3chd.b 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.1 0.1
0
0.1 0.1
[1] 3che.b 0.2 0.3 0.1 0.2 0.2 0.2 0.2 0.2 0.1 0.1 0.1
0
0.1
[1] 3chf.b 0.2 0.3 0.1 0.2 0.2 0.3 0.2 0.2 0.1 0.1 0.1 0.1
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
1w9p.b
1w9u.a
1w9v.b
2a3a.b
2a3b.b
2a3c.a
2a3e.a
2iuz.b
3ch9.b
3chc.b
3chd.b
3che.b
3chf.b
[1] 1w9p.b
0
1.5 1.4 1.1 1.1 1.5 1.4 1.1 1.4 0.4 0.5 1.3 1.4
[1] 1w9u.a 1.5
0
0.8 1.3 1.3 1.5 0.8 1.3 0.7 1.4 1.4 0.8 0.8
[1] 1w9v.b 1.4 0.8
0
1.3 1.3 1.5 0.5 1.3 0.5 1.4 1.3 0.4 0.5
[1] 2a3a.b 1.1 1.3 1.3
0
0.3 1.0 1.2 0.2 1.1 1.0 1.0 1.2 1.2
[1] 2a3b.b 1.1 1.3 1.3 0.3
0
1.0 1.3 0.2 1.1 1.0 1.1 1.2 1.2
[1] 2a3c.a 1.5 1.5 1.5 1.0 1.0
0
1.5 1.0 1.4 1.4 1.4 1.5 1.5
[1] 2a3e.a 1.4 0.8 0.5 1.2 1.3 1.5
0
1.2 0.4 1.3 1.4 0.4 0.4
[1] 2iuz.b 1.1 1.3 1.3 0.2 0.2 1.0 1.2
0
1.1 1.0 1.1 1.2 1.2
[1] 3ch9.b 1.4 0.7 0.5 1.1 1.1 1.4 0.4 1.1
0
1.2 1.3 0.3 0.3
[1] 3chc.b 0.4 1.4 1.4 1.0 1.0 1.4 1.3 1.0 1.2
0
0.5 1.3 1.3
[1] 3chd.b 0.5 1.4 1.3 1.0 1.1 1.4 1.4 1.1 1.3 0.5
0
1.3 1.3
[1] 3che.b 1.3 0.8 0.4 1.2 1.2 1.5 0.4 1.2 0.3 1.3 1.3
0
0.1
[1] 3chf.b 1.4 0.8 0.5 1.2 1.2 1.5 0.4 1.2 0.3 1.3 1.3 0.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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