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CBPT_THEVU_99_423

Carboxypeptidase T [Peptidase M14 family]

Composition of the binding site

Protein chains monomer
A1 (CBPT_THEVU):167, 169, 170, 227, 244, 245, 302:305, 309, 313, 349, 352, 353, 355, 358, 360, 361, 373, 375, 385167, 169, 170, 227, 244, 245, 302:305, 309, 313, 349, 352, 353, 355, 358, 360, 361, 373, 375, 385
Metals (Me):Zn

Full PDB list

1obr, 3prt, 3qnv, 3v38, 3v7z, 4djl, 4duk, 4f8z, 4gm5, 4iav, 4ihm, 4ik2, 5myh (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
1
6
7
R
1
6
9
E
1
7
0
R
2
2
7
N
2
4
4
R
2
4
5
H
3
0
2
T
3
0
3
Y
3
0
4
S
3
0
5
L
3
0
9
G
3
1
3
A
3
4
9
L
3
5
2
Y
3
5
3
T
3
5
5
D
3
5
8
T
3
6
0
D
3
6
1
T
3
7
3
E
3
7
5
F
3
8
5
[1]3prt.a none . . . . . . . . . . . S G . . A G D . . . . Zn
[1]3qnv.a none . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3v38.a none . . . . . . . . . . . . . N . . . . . . . . Zn
[1]3v7z.a gem15 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4djl.a cxa16 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4duk.a bzs15 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4f8z.a bl216 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4gm5.a 0x916 . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4iav.a cxa16 . . . . . . . . . . . S G . . A G D . . . . Zn
[1]4ihm.a none . . . . . . . . . . . S G . . A G - . . . . Zn
[1]4ik2.a bl216 . . . . . . . . . . . S G . . A G D . . . . Zn
[1]5myh.a 3k014 . . . . . . . . . . . . . . . . . . . . . . Zn

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 Me
H
1
6
7
R
1
6
9
E
1
7
0
R
2
2
7
N
2
4
4
R
2
4
5
H
3
0
2
T
3
0
3
Y
3
0
4
S
3
0
5
L
3
0
9
G
3
1
3
A
3
4
9
L
3
5
2
Y
3
5
3
T
3
5
5
D
3
5
8
T
3
6
0
D
3
6
1
T
3
7
3
E
3
7
5
F
3
8
5
[1]3prt.a . . . . . . . . . . . S G . . A G D . . . . Zn
[1]3qnv.a . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3v38.a . . . . . . . . . . . . . N . . . . . . . . Zn
[1]3v7z.a . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4djl.a . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4duk.a . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4f8z.a . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4gm5.a . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4iav.a . . . . . . . . . . . S G . . A G D . . . . Zn
[1]4ihm.a . . . . . . . . . . . S G . . A G - . . . . Zn
[1]4ik2.a . . . . . . . . . . . S G . . A G D . . . . Zn
[1]5myh.a . . . . . . . . . . . . . . . . . . . . . . Zn

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
3prt.a is apo
3qnv.a is apo
3v38.a is apo
3v7z.a:gem
4djl.a:cxa
4duk.a:bzs
4f8z.a:bl2
4gm5.a:0x9
4iav.a:cxa
4ihm.a is apo
4ik2.a:bl2
5myh.a:3k0
[1] 3prt.a
-
- - 0.3 0.3 0.2 0 0.4 0.1 - 0 0.1
[1] 3qnv.a -
-
- 0.2 0.1 0.1 0.1 0.1 0.4 - 0.1 0.2
[1] 3v38.a - -
-
0.3 0.2 0.2 0.1 0.2 0.3 - 0 0.2
[1] 3v7z.a - - -
0
0.1 0 0 0 0.2 - 0 0.1
[1] 4djl.a - - - 0.4
0
0.2 0.1 0.1 0.6 - 0.1 0.1
[1] 4duk.a - - - 0.1 0.1
0
0 0.1 0.7 - 0 0.1
[1] 4f8z.a - - - 0.4 0.2 0
0.1
0.1 0.8 - 0 0.2
[1] 4gm5.a - - - 0.1 0.3 0.1 0
0
0.2 - 0 0.2
[1] 4iav.a - - - 0.3 0.3 0.1 0 0.9
0
- 0 0.1
[1] 4ihm.a - - - 0.3 0.3 0.2 0 0.2 0.1
-
0 0.2
[1] 4ik2.a - - - 0.5 0.4 0.2 0 1.4 0.7 -
0
0.2
[1] 5myh.a - - - 0 0.2 0 0 0.1 0.2 - 0
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
3prt.a
3qnv.a
3v38.a
3v7z.a
4djl.a
4duk.a
4f8z.a
4gm5.a
4iav.a
4ihm.a
4ik2.a
5myh.a
[1] 3prt.a
0
.04 .03 .03 .05 .04 .05 .04 .04 .02 .08 .03
[1] 3qnv.a .04
0
.01 .01 .03 .04 .03 .01 .06 .03 .10 .01
[1] 3v38.a .03 .01
0
.02 .03 .03 .03 .02 .06 .03 .10 .01
[1] 3v7z.a .03 .01 .02
0
.05 .03 .05 .02 .06 .03 .10 .01
[1] 4djl.a .05 .03 .03 .05
0
.02 .02 .03 .08 .05 .09 .03
[1] 4duk.a .04 .04 .03 .03 .02
0
.01 .03 .08 .05 .07 .03
[1] 4f8z.a .05 .03 .03 .05 .02 .01
0
.04 .09 .05 .07 .03
[1] 4gm5.a .04 .01 .02 .02 .03 .03 .04
0
.05 .02 .10 .01
[1] 4iav.a .04 .06 .06 .06 .08 .08 .09 .05
0
.03 .05 .06
[1] 4ihm.a .02 .03 .03 .03 .05 .05 .05 .02 .03
0
.09 .03
[1] 4ik2.a .08 .10 .10 .10 .09 .07 .07 .10 .05 .09
0
.09
[1] 5myh.a .03 .01 .01 .01 .03 .03 .03 .01 .06 .03 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3prt.a
3qnv.a
3v38.a
3v7z.a
4djl.a
4duk.a
4f8z.a
4gm5.a
4iav.a
4ihm.a
4ik2.a
5myh.a
[1] 3prt.a
0
0.2 0.2 0.2 0.3 0.3 0.4 0.3 0.2 0.1 0.4 0.2
[1] 3qnv.a 0.2
0
0.2 0.1 0.2 0.2 0.3 0.1 0.2 0.2 0.4 0.1
[1] 3v38.a 0.2 0.2
0
0.2 0.3 0.3 0.4 0.3 0.2 0.2 0.4 0.2
[1] 3v7z.a 0.2 0.1 0.2
0
0.2 0.2 0.3 0.1 0.2 0.2 0.4 0.1
[1] 4djl.a 0.3 0.2 0.3 0.2
0
0.1 0.1 0.1 0.2 0.3 0.3 0.1
[1] 4duk.a 0.3 0.2 0.3 0.2 0.1
0
0.1 0.2 0.3 0.4 0.2 0.1
[1] 4f8z.a 0.4 0.3 0.4 0.3 0.1 0.1
0
0.2 0.3 0.4 0.2 0.2
[1] 4gm5.a 0.3 0.1 0.3 0.1 0.1 0.2 0.2
0
0.2 0.3 0.3 0.1
[1] 4iav.a 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.2
0
0.2 0.3 0.2
[1] 4ihm.a 0.1 0.2 0.2 0.2 0.3 0.4 0.4 0.3 0.2
0
0.5 0.3
[1] 4ik2.a 0.4 0.4 0.4 0.4 0.3 0.2 0.2 0.3 0.3 0.5
0
0.3
[1] 5myh.a 0.2 0.1 0.2 0.1 0.1 0.1 0.2 0.1 0.2 0.3 0.3
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
3prt.a
3qnv.a
3v38.a
3v7z.a
4djl.a
4duk.a
4f8z.a
4gm5.a
4iav.a
4ihm.a
4ik2.a
5myh.a
[1] 3prt.a
0
0.3 0.2 0.4 0.5 0.6 0.6 0.4 0.5 0.2 0.7 0.5
[1] 3qnv.a 0.3
0
0.3 0.4 0.3 0.5 0.4 0.3 0.4 0.4 0.5 0.4
[1] 3v38.a 0.2 0.3
0
0.3 0.3 0.4 0.4 0.3 0.3 0.2 0.5 0.4
[1] 3v7z.a 0.4 0.4 0.3
0
0.4 0.5 0.5 0.3 0.2 0.4 0.6 0.6
[1] 4djl.a 0.5 0.3 0.3 0.4
0
0.3 0.1 0.2 0.4 0.6 0.3 0.5
[1] 4duk.a 0.6 0.5 0.4 0.5 0.3
0
0.3 0.4 0.5 0.6 0.2 0.5
[1] 4f8z.a 0.6 0.4 0.4 0.5 0.1 0.3
0
0.2 0.5 0.6 0.2 0.5
[1] 4gm5.a 0.4 0.3 0.3 0.3 0.2 0.4 0.2
0
0.3 0.5 0.4 0.5
[1] 4iav.a 0.5 0.4 0.3 0.2 0.4 0.5 0.5 0.3
0
0.4 0.6 0.6
[1] 4ihm.a 0.2 0.4 0.2 0.4 0.6 0.6 0.6 0.5 0.4
0
0.7 0.6
[1] 4ik2.a 0.7 0.5 0.5 0.6 0.3 0.2 0.2 0.4 0.6 0.7
0
0.6
[1] 5myh.a 0.5 0.4 0.4 0.6 0.5 0.5 0.5 0.5 0.6 0.6 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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