If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

CBPB2_HUMAN_115_423

Carboxypeptidase B2 [Peptidase M14 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CBPB2_HUMAN):R: Substrate binding (181, 184)
R: Substrate binding (256, 257)
R: Substrate binding (311, 312)
54, 55, 57, 239, 310, 313, 321, 362, 363, 365, 368, 370, 383, 385, 394
54, 55, 57, 181, 184, 239, 256, 257, 310:313, 321, 362, 363, 365, 368, 370, 383, 385, 394
Metals (Me):Zn

Full PDB list

3d66, 3d67, 3d68, 3lms, 4p10, 5hvf, 5hvg, 5hvh (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Q
5
5
H
1
8
1
E
1
8
4
R
2
3
9
N
2
5
6
R
2
5
7
H
3
1
0
S
3
1
1
Y
3
1
2
S
3
1
3
S
3
2
1
L
3
6
2
Y
3
6
3
A
3
6
5
D
3
7
0
T
3
8
3
E
3
8
5
F
3
9
4
[1]3d67.c gem15 . . . . . . . . . . . . . . . . . . Zn
[1]3d68.c R12 . . . . . . . . . . . . . . . . . . Zn
[1]3lms.a G,L14 - . . . . . . . . . . . . . . . . . Zn
[1]4p10.a 2b819 . . . . . . . . . . . . . . . . . . Zn
[1]5hvf.a none . . . . . . . . . . . . . . . . . . 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
W
5
4
Q
5
5
V
5
7
H
1
8
1
E
1
8
4
R
2
3
9
N
2
5
6
R
2
5
7
H
3
1
0
S
3
1
1
Y
3
1
2
S
3
1
3
S
3
2
1
L
3
6
2
Y
3
6
3
A
3
6
5
G
3
6
8
D
3
7
0
T
3
8
3
E
3
8
5
F
3
9
4
[1]3d67.c . . . . . . . . . . . . . . . . . . . . . Zn
[1]3d68.c . . . . . . . . . . . . . . . . . . . . . Zn
[1]3lms.a - - - . . . . . . . . . . . . . . . . . . Zn
[1]4p10.a . . . . . . . . . . . . . . . . . . . . . Zn
[1]5hvf.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3d67.c:gem
3d68.c:R
3lms.a:G,L
4p10.a:2b8
5hvf.a is apo
[1] 3d67.c
0.1
0.1 0.3 0.3 -
[1] 3d68.c 0.5
0
0.3 0.3 -
[1] 3lms.a 0.6 0.3
0
0.3 -
[1] 4p10.a 0.6 0.2 0.2
0
-
[1] 5hvf.a 0.7 0.1 0.2 0.2
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3d67.c
3d68.c
3lms.a
4p10.a
5hvf.a
[1] 3d67.c
0
.03 .04 .05 .05
[1] 3d68.c .03
0
.03 .04 .04
[1] 3lms.a .04 .03
0
.03 .02
[1] 4p10.a .05 .04 .03
0
.03
[1] 5hvf.a .05 .04 .02 .03
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

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
3d67.c
3d68.c
3lms.a
4p10.a
5hvf.a
[1] 3d67.c
0
0.5 0.5 0.7 0.5
[1] 3d68.c 0.5
0
0.4 0.6 0.5
[1] 3lms.a 0.5 0.4
0
0.6 0.3
[1] 4p10.a 0.7 0.6 0.6
0
0.7
[1] 5hvf.a 0.5 0.5 0.3 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
3d67.c
3d68.c
3lms.a
4p10.a
5hvf.a
[1] 3d67.c
0
0.7 0.7 1.5 0.9
[1] 3d68.c 0.7
0
0.8 1.5 1.0
[1] 3lms.a 0.7 0.8
0
1.6 0.8
[1] 4p10.a 1.5 1.5 1.6
0
1.6
[1] 5hvf.a 0.9 1.0 0.8 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...