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CATB_BOVIN_126_334

Cathepsin B [Peptidase C1 family]

Composition of the binding site

Protein chains monomer
A1 (CATB_BOVIN):102:109, 147, 148, 151:155, 189, 190, 198:201, 252, 255, 260, 275:279, 300, 324102:109, 147, 148, 151:155, 189, 190, 198:201, 252, 255, 260, 275:279, 300, 324

Full PDB list

1ito, 1qdq, 1sp4, 2dc6, 2dc7, 2dc8, 2dc9, 2dca, 2dcb, 2dcc, 2dcd

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Q
1
0
2
G
1
0
3
S
1
0
4
C
1
0
5
G
1
0
6
S
1
0
7
C
1
0
8
W
1
0
9
G
1
4
7
G
1
5
2
G
1
5
3
F
1
5
4
P
1
5
5
H
1
8
9
H
1
9
0
C
1
9
8
G
2
0
0
E
2
0
1
A
2
5
2
V
2
5
5
L
2
6
0
M
2
7
5
G
2
7
7
H
2
7
8
A
2
7
9
W
3
0
0
E
3
2
4
[1]1ito.a e6c22 . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]1qdq.a 07417 . . . . . . * . . . . E . . . . . . . . . . . . . . .
[1]1sp4.b ep241 - - - - - - - - . . . . . . . . . . . . . . . . . . .
[1]2dc6.a 73v34 . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]2dc7.a 04226 . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]2dc8.a 59a19 . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]2dc9.a 74m28 . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]2dca.a 75v24 . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]2dcb.a 76v27 . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]2dcc.a 77b38 . . . . . . * . . . . . . . . . . . . . . . . . . . .
[1]2dcd.a 78a31 . . . . . . * . . . . . . . . . . . . . . . . . . . .

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
Q
1
0
2
G
1
0
3
S
1
0
4
C
1
0
5
G
1
0
6
S
1
0
7
C
1
0
8
W
1
0
9
G
1
4
7
D
1
4
8
N
1
5
1
G
1
5
2
G
1
5
3
F
1
5
4
P
1
5
5
H
1
8
9
H
1
9
0
C
1
9
8
T
1
9
9
G
2
0
0
E
2
0
1
A
2
5
2
V
2
5
5
L
2
6
0
M
2
7
5
G
2
7
6
G
2
7
7
H
2
7
8
A
2
7
9
W
3
0
0
E
3
2
4
[1]1ito.a . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]1qdq.a . . . . . . * . . . . . . E . . . . . . . . . . . . . . . . .
[1]1sp4.b - - - - - - - - . . . . . . . . * . . . . . . . . . . . . . .
[1]2dc6.a . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]2dc7.a . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]2dc8.a . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]2dc9.a . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]2dca.a . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]2dcb.a . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]2dcc.a . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]2dcd.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
1ito.a:e6c
1qdq.a:074
1sp4.b:ep2
2dc6.a:73v
2dc7.a:042
2dc8.a:59a
2dc9.a:74m
2dca.a:75v
2dcb.a:76v
2dcc.a:77b
2dcd.a:78a
[1] 1ito.a
0.5
0.3 0.4 0.3 0.4 0.4 0.5 0.4 0.4 0.3 0.5
[1] 1qdq.a 0.7
0.3
0.6 0.6 0.7 0.6 1.2 0.8 0.9 0.5 0.8
[1] 1sp4.b 0 0
0.1
0 0.3 0 0.7 0.2 0.5 0.4 0.1
[1] 2dc6.a 0.6 0.3 0.4
0.3
0.6 0.3 0.6 0.7 0.4 0.3 0.5
[1] 2dc7.a 0.5 0.3 0.4 0.3
0.3
0.4 0.7 0.4 0.3 0.3 0.6
[1] 2dc8.a 0.8 0.3 0.6 0.5 0.5
0.3
0.9 0.6 0.5 0.3 0.7
[1] 2dc9.a 0.8 0.3 0.4 0.3 0.6 0.3
0.7
0.6 0.5 0.3 0.5
[1] 2dca.a 0.5 0.3 0.4 0.3 0.5 0.3 0.8
0.5
0.5 0.3 0.5
[1] 2dcb.a 0.5 0.3 0.4 0.3 0.4 0.4 0.8 0.4
0.3
0.3 0.5
[1] 2dcc.a 0.8 0.3 0.7 0.5 0.5 0.5 0.6 0.6 0.5
0.3
0.7
[1] 2dcd.a 0.8 0.3 0.3 0.3 0.6 0.3 0.8 0.6 0.5 0.3
0.4
[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
1ito.a
1qdq.a
1sp4.b
2dc6.a
2dc7.a
2dc8.a
2dc9.a
2dca.a
2dcb.a
2dcc.a
2dcd.a
[1] 1ito.a
0
.04 .06 .02 .02 .02 .03 .03 .02 .02 .03
[1] 1qdq.a .04
0
.04 .02 .04 .02 .02 .03 .03 .03 .02
[1] 1sp4.b .06 .04
0
.05 .05 .05 .06 .05 .05 .07 .05
[1] 2dc6.a .02 .02 .05
0
.02 .01 .01 .02 .03 .01 .01
[1] 2dc7.a .02 .04 .05 .02
0
.02 .02 .01 .01 .03 .03
[1] 2dc8.a .02 .02 .05 .01 .02
0
0 .02 .02 .01 .01
[1] 2dc9.a .03 .02 .06 .01 .02 0
0
.01 .02 .02 .01
[1] 2dca.a .03 .03 .05 .02 .01 .02 .01
0
0 .03 .02
[1] 2dcb.a .02 .03 .05 .03 .01 .02 .02 0
0
.03 .02
[1] 2dcc.a .02 .03 .07 .01 .03 .01 .02 .03 .03
0
.02
[1] 2dcd.a .03 .02 .05 .01 .03 .01 .01 .02 .02 .02
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
1ito.a
1qdq.a
1sp4.b
2dc6.a
2dc7.a
2dc8.a
2dc9.a
2dca.a
2dcb.a
2dcc.a
2dcd.a
[1] 1ito.a
0
0.7 0.8 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.4
[1] 1qdq.a 0.7
0
0.5 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6
[1] 1sp4.b 0.8 0.5
0
0.7 0.8 0.8 0.8 0.7 0.8 0.7 0.7
[1] 2dc6.a 0.4 0.6 0.7
0
0.4 0.4 0.3 0.4 0.4 0.3 0.2
[1] 2dc7.a 0.3 0.6 0.8 0.4
0
0.1 0.2 0.2 0.1 0.3 0.4
[1] 2dc8.a 0.3 0.6 0.8 0.4 0.1
0
0.1 0.2 0.1 0.3 0.4
[1] 2dc9.a 0.3 0.6 0.8 0.3 0.2 0.1
0
0.1 0.2 0.2 0.3
[1] 2dca.a 0.3 0.6 0.7 0.4 0.2 0.2 0.1
0
0.2 0.2 0.3
[1] 2dcb.a 0.3 0.6 0.8 0.4 0.1 0.1 0.2 0.2
0
0.3 0.4
[1] 2dcc.a 0.3 0.6 0.7 0.3 0.3 0.3 0.2 0.2 0.3
0
0.3
[1] 2dcd.a 0.4 0.6 0.7 0.2 0.4 0.4 0.3 0.3 0.4 0.3
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
1ito.a
1qdq.a
1sp4.b
2dc6.a
2dc7.a
2dc8.a
2dc9.a
2dca.a
2dcb.a
2dcc.a
2dcd.a
[1] 1ito.a
0
1.5 1.4 0.5 0.4 0.4 0.6 0.4 0.4 0.5 0.5
[1] 1qdq.a 1.5
0
0.7 1.4 1.6 1.5 1.6 1.5 1.6 1.6 1.4
[1] 1sp4.b 1.4 0.7
0
1.2 1.4 1.3 1.4 1.3 1.4 1.4 1.2
[1] 2dc6.a 0.5 1.4 1.2
0
0.5 0.4 0.6 0.4 0.5 0.4 0.3
[1] 2dc7.a 0.4 1.6 1.4 0.5
0
0.2 0.5 0.3 0.1 0.4 0.5
[1] 2dc8.a 0.4 1.5 1.3 0.4 0.2
0
0.5 0.2 0.2 0.4 0.4
[1] 2dc9.a 0.6 1.6 1.4 0.6 0.5 0.5
0
0.5 0.4 0.5 0.6
[1] 2dca.a 0.4 1.5 1.3 0.4 0.3 0.2 0.5
0
0.2 0.4 0.3
[1] 2dcb.a 0.4 1.6 1.4 0.5 0.1 0.2 0.4 0.2
0
0.4 0.4
[1] 2dcc.a 0.5 1.6 1.4 0.4 0.4 0.4 0.5 0.4 0.4
0
0.5
[1] 2dcd.a 0.5 1.4 1.2 0.3 0.5 0.4 0.6 0.3 0.4 0.5
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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