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CBPA1_HUMAN_111_419

Carboxypeptidase A1 [Peptidase M14 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CBPA1_HUMAN):R: Substrate binding (179, 181, 182)
R: Substrate binding (254, 255)
R: Substrate binding (307, 308)
51:56, 64, 237, 273, 274, 306, 309, 313, 353, 357, 358, 360, 363, 378, 380, 389
51:56, 64, 179, 181, 182, 237, 254, 255, 273, 274, 306:309, 313, 353, 357, 358, 360, 363, 378, 380, 389
Metals (Me):Zn

Full PDB list

2v77, 3fju, 4uee, 4uef, 4uez, 4uf4, 5om9

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
R
5
4
H
1
7
9
R
1
8
1
E
1
8
2
R
2
3
7
N
2
5
4
R
2
5
5
E
2
7
3
T
2
7
4
H
3
0
6
S
3
0
7
Y
3
0
8
S
3
0
9
M
3
1
3
I
3
5
3
I
3
5
7
Y
3
5
8
A
3
6
0
S
3
6
3
T
3
7
8
E
3
8
0
F
3
8
9
[1]2v77.a pay20 - . . . . . . . . . . . . . . . . . . . . . Zn
[1]3fju.a DLL25 - . . . . . . . . . . . . . . . . . . . . . Zn
[1]4uee.a la930 - . . . . . . . . . . . . . . . . . . . . . Zn
[1]4uef.a tje34 - . . . . . . . . . . . . . . . . . . . . . Zn
[1]4uez.a lff35 - . . . . . . . . . . . . . . . . . . . . . Zn
[2]4uf4.b o2v11 . . . . . . . . . . . . . . . . . . . . * . Zn
[2]5om9.b o2s11 . . . . . . . . . . . . . . . . . . . . * . 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
D
5
1
F
5
2
W
5
3
R
5
4
G
5
5
P
5
6
D
6
4
H
1
7
9
R
1
8
1
E
1
8
2
R
2
3
7
N
2
5
4
R
2
5
5
E
2
7
3
T
2
7
4
H
3
0
6
S
3
0
7
Y
3
0
8
S
3
0
9
M
3
1
3
I
3
5
3
I
3
5
7
Y
3
5
8
A
3
6
0
S
3
6
3
T
3
7
8
E
3
8
0
F
3
8
9
[1]2v77.a - - - - - - - . . . . . . . . . . . . . . . . . . . . . Zn
[1]3fju.a - - - - - - - . . . . . . . . . . . . . . . . . . . . . Zn
[1]4uee.a - - - - - - - . . . . . . . . . . . . . . . . . . . . . Zn
[1]4uef.a - - - - - - - . . . . . . . . . . . . . . . . . . . . . Zn
[1]4uez.a - - - - - - - . . . . . . . . . . . . . . . . . . . . . Zn
[2]4uf4.b . . * * * . . . . . . . . . . . . . . . . . . . . . * . Zn
[2]5om9.b . . * * * . . . . . . . . . . . . . . . . . . . . . * . 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
2v77.a:pay
3fju.a:DLL
4uee.a:la9
4uef.a:tje
4uez.a:lff
4uf4.b:o2v
5om9.b:o2s
[1] 2v77.a
0
0.5 0.4 0.3 0.4 0.4 0.4
[1] 3fju.a 0.2
0
0.8 0.5 0.5 0.4 0.5
[1] 4uee.a 0.3 0.5
0
0 0.3 0.5 0.5
[1] 4uef.a 0.1 0.3 0.1
0
0.1 0.4 0.4
[1] 4uez.a 0.1 0.1 0.2 0.2
0.1
0.4 0.4
[2] 4uf4.b 1.7 7.3 5.8 5.4 8.1
0.7
0.9
[2] 5om9.b 1.9 7.6 6.0 5.8 7.3 0.9
0.9
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
2v77.a
3fju.a
4uee.a
4uef.a
4uez.a
4uf4.b
5om9.b
[1] 2v77.a
0
.01 .03 .03 .03 .32 .32
[1] 3fju.a .01
0
.03 .03 .02 .33 .33
[1] 4uee.a .03 .03
0
.02 .03 .34 .34
[1] 4uef.a .03 .03 .02
0
.01 .32 .32
[1] 4uez.a .03 .02 .03 .01
0
.32 .32
[2] 4uf4.b .32 .33 .34 .32 .32
0
0
[2] 5om9.b .32 .33 .34 .32 .32 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
2v77.a
3fju.a
4uee.a
4uef.a
4uez.a
4uf4.b
5om9.b
[1] 2v77.a
0
0.2 0.2 0.1 0.2 0.3 0.3
[1] 3fju.a 0.2
0
0.3 0.2 0.2 0.4 0.4
[1] 4uee.a 0.2 0.3
0
0.1 0.2 0.3 0.3
[1] 4uef.a 0.1 0.2 0.1
0
0.2 0.3 0.3
[1] 4uez.a 0.2 0.2 0.2 0.2
0
0.3 0.3
[2] 4uf4.b 0.3 0.4 0.3 0.3 0.3
0
0.1
[2] 5om9.b 0.3 0.4 0.3 0.3 0.3 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

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
2v77.a
3fju.a
4uee.a
4uef.a
4uez.a
4uf4.b
5om9.b
[1] 2v77.a
0
0.5 0.8 0.7 0.8 0.9 1.0
[1] 3fju.a 0.5
0
0.9 0.8 0.9 1.0 1.1
[1] 4uee.a 0.8 0.9
0
0.4 0.3 0.8 0.8
[1] 4uef.a 0.7 0.8 0.4
0
0.5 0.6 0.7
[1] 4uez.a 0.8 0.9 0.3 0.5
0
0.7 0.8
[2] 4uf4.b 0.9 1.0 0.8 0.6 0.7
0
0.3
[2] 5om9.b 1.0 1.1 0.8 0.7 0.8 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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