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DAC_STRSR_32_380

D-alanyl-D-alanine carboxypeptidase [Peptidase S12 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DAC_STRSR):R: Substrate binding (151, 152, 154)
R: Substrate binding (190, 192)
R: Substrate binding (330:332)
R: Substrate binding (357, 358)
92, 93, 96, 147, 148, 245, 264, 265, 268, 269, 306, 309, 316, 329, 333, 334, 337, 339, 360, 363
92, 93, 96, 147, 148, 151, 152, 154, 190, 192, 245, 264, 265, 268, 269, 306, 309, 316, 329:334, 337, 339, 357, 358, 360, 363

Full PDB list

1cef, 1ceg, 1hvb, 1ikg, 1iki, 1mpl, 1pw1, 1pw8, 1pwc, 1pwd, 1pwg, 1scw, 1sde, 1yqs, 3pte

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
9
2
S
9
3
K
9
6
T
1
4
7
N
1
4
8
F
1
5
1
T
1
5
4
Y
1
9
0
N
1
9
2
L
2
4
5
W
2
6
4
A
2
6
5
A
2
6
8
G
2
6
9
N
3
0
6
Q
3
0
9
R
3
1
6
H
3
2
9
T
3
3
0
G
3
3
1
T
3
3
2
V
3
3
3
Q
3
3
4
Y
3
3
7
Y
3
3
9
S
3
5
7
N
3
5
8
V
3
6
0
L
3
6
3
[1]1cef.a cef26 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ceg.a cep22 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1hvb.a ceh51 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ikg.a rex26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1iki.a dal,rey27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1mpl.a re121 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pw1.a hel29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pw8.a h2a29 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pwc.a pnm23 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pwd.a csc24 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pwg.a he029 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1scw.a cp515 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1sde.a 2pb13 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1yqs.a bsa,bsa29 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3pte.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
G
9
2
S
9
3
K
9
6
T
1
4
7
N
1
4
8
F
1
5
1
A
1
5
2
T
1
5
4
Y
1
9
0
N
1
9
2
L
2
4
5
W
2
6
4
A
2
6
5
A
2
6
8
G
2
6
9
N
3
0
6
Q
3
0
9
R
3
1
6
H
3
2
9
T
3
3
0
G
3
3
1
T
3
3
2
V
3
3
3
Q
3
3
4
Y
3
3
7
Y
3
3
9
S
3
5
7
N
3
5
8
V
3
6
0
L
3
6
3
[1]1cef.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ceg.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1hvb.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ikg.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1iki.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1mpl.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pw1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pw8.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pwc.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pwd.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1pwg.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1scw.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1sde.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1yqs.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3pte.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
1cef.a:cef
1ceg.a:cep
1hvb.a:ceh
1ikg.a:rex
1iki.a:dal,rey
1mpl.a:re1
1pw1.a:hel
1pw8.a:h2a
1pwc.a:pnm
1pwd.a:csc
1pwg.a:he0
1scw.a:cp5
1sde.a:2pb
1yqs.a:bsa
3pte.a is apo
[1] 1cef.a
0.8
0.9 0.8 1.0 0.8 1.1 0.6 0.9 0.6 0.6 1.1 0.9 0.7 0.2 -
[1] 1ceg.a 0.8
0.9
0.7 1.1 0.8 1.2 0.8 0.8 0.6 0.5 0.9 0.7 0.7 0.4 -
[1] 1hvb.a 1.0 1.0
0.9
1.2 1.0 1.1 0.9 0.9 1.1 0.8 1.2 0.5 0.7 0.5 -
[1] 1ikg.a 0.8 0.5 0.3
0.1
0.5 0.3 0.4 0.4 0.5 0.3 0.6 0.2 0.2 0.2 -
[1] 1iki.a 0.9 0.5 0.7 1.2
0.5
0.9 0.4 0.6 0.9 0.5 0.8 0.2 0.4 0.3 -
[1] 1mpl.a 0.8 0.7 0.7 1.2 0.7
0.6
0.5 0.6 0.7 0.5 1.1 0.3 0.4 0.3 -
[1] 1pw1.a 0.7 0.4 0.4 0.3 0.9 0.8
0.2
0.4 0.4 0.3 0.7 0.4 0.4 0.5 -
[1] 1pw8.a 1.0 1.0 0.9 0.9 0.7 1.0 0.5
0.7
0.8 0.6 0.8 0.6 0.5 0.5 -
[1] 1pwc.a 0.8 0.9 0.9 0.9 1.0 1.1 0.7 0.7
0.7
0.6 1.0 0.6 0.6 0.5 -
[1] 1pwd.a 0.8 0.9 0.7 1.1 1.0 1.2 0.7 0.8 0.8
0.6
1.0 0.7 0.6 0.5 -
[1] 1pwg.a 0.6 0.8 0.7 0.9 0.8 1.0 0.5 0.7 0.8 0.6
0.8
0.6 0.5 0.5 -
[1] 1scw.a 1.4 1.0 1.1 1.9 1.4 1.3 0.9 1.2 1.2 1.2 1.4
0.4
0.6 0.5 -
[1] 1sde.a 1.2 1.0 1.1 1.5 1.0 1.2 1.0 1.1 1.1 0.8 1.5 0.4
0.4
0.4 -
[1] 1yqs.a 1.0 1.0 1.0 1.6 1.1 1.2 1.0 0.9 1.0 0.7 1.4 0.8 1.0
0.5
-
[1] 3pte.a 1.2 1.0 1.2 1.7 1.0 1.5 1.1 1.2 1.1 1.1 1.3 1.2 1.2 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
1cef.a
1ceg.a
1hvb.a
1ikg.a
1iki.a
1mpl.a
1pw1.a
1pw8.a
1pwc.a
1pwd.a
1pwg.a
1scw.a
1sde.a
1yqs.a
3pte.a
[1] 1cef.a
0
.01 .03 .06 .04 .05 .04 .03 .02 .03 .03 .03 .04 .03 .03
[1] 1ceg.a .01
0
.02 .04 .03 .04 .03 .02 .01 .01 .02 .02 .03 .03 .03
[1] 1hvb.a .03 .02
0
.04 .02 .03 .03 0 .01 .01 .01 .02 .02 .05 .04
[1] 1ikg.a .06 .04 .04
0
.04 .02 .04 .05 .04 .04 .04 .04 .05 .05 .06
[1] 1iki.a .04 .03 .02 .04
0
.03 .03 .02 .03 .02 .02 .02 .02 .03 .03
[1] 1mpl.a .05 .04 .03 .02 .03
0
.03 .04 .03 .03 .03 .03 .02 .03 .05
[1] 1pw1.a .04 .03 .03 .04 .03 .03
0
.02 .02 .03 .02 .04 .04 .05 .05
[1] 1pw8.a .03 .02 0 .05 .02 .04 .02
0
.01 .02 0 .03 .03 .05 .04
[1] 1pwc.a .02 .01 .01 .04 .03 .03 .02 .01
0
.01 .01 .02 .03 .04 .03
[1] 1pwd.a .03 .01 .01 .04 .02 .03 .03 .02 .01
0
.01 .02 .02 .03 .03
[1] 1pwg.a .03 .02 .01 .04 .02 .03 .02 0 .01 .01
0
.02 .03 .05 .04
[1] 1scw.a .03 .02 .02 .04 .02 .03 .04 .03 .02 .02 .02
0
.01 .03 .02
[1] 1sde.a .04 .03 .02 .05 .02 .02 .04 .03 .03 .02 .03 .01
0
.03 .04
[1] 1yqs.a .03 .03 .05 .05 .03 .03 .05 .05 .04 .03 .05 .03 .03
0
.02
[1] 3pte.a .03 .03 .04 .06 .03 .05 .05 .04 .03 .03 .04 .02 .04 .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
1cef.a
1ceg.a
1hvb.a
1ikg.a
1iki.a
1mpl.a
1pw1.a
1pw8.a
1pwc.a
1pwd.a
1pwg.a
1scw.a
1sde.a
1yqs.a
3pte.a
[1] 1cef.a
0
0.2 0.4 0.3 0.3 0.3 0.2 0.2 0.2 0.2 0.2 0.4 0.4 0.2 0.2
[1] 1ceg.a 0.2
0
0.4 0.3 0.3 0.2 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.1
[1] 1hvb.a 0.4 0.4
0
0.5 0.3 0.4 0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.4 0.4
[1] 1ikg.a 0.3 0.3 0.5
0
0.3 0.2 0.2 0.3 0.3 0.3 0.3 0.5 0.4 0.4 0.3
[1] 1iki.a 0.3 0.3 0.3 0.3
0
0.3 0.3 0.3 0.3 0.2 0.3 0.3 0.2 0.4 0.4
[1] 1mpl.a 0.3 0.2 0.4 0.2 0.3
0
0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.3 0.3
[1] 1pw1.a 0.2 0.2 0.4 0.2 0.3 0.2
0
0.2 0.2 0.2 0.2 0.4 0.4 0.3 0.2
[1] 1pw8.a 0.2 0.2 0.4 0.3 0.3 0.2 0.2
0
0.1 0.1 0.1 0.3 0.3 0.3 0.3
[1] 1pwc.a 0.2 0.2 0.4 0.3 0.3 0.2 0.2 0.1
0
0.1 0.1 0.4 0.3 0.3 0.3
[1] 1pwd.a 0.2 0.2 0.3 0.3 0.2 0.2 0.2 0.1 0.1
0
0.1 0.4 0.3 0.3 0.2
[1] 1pwg.a 0.2 0.2 0.3 0.3 0.3 0.2 0.2 0.1 0.1 0.1
0
0.4 0.3 0.3 0.3
[1] 1scw.a 0.4 0.4 0.3 0.5 0.3 0.4 0.4 0.3 0.4 0.4 0.4
0
0.2 0.5 0.5
[1] 1sde.a 0.4 0.3 0.3 0.4 0.2 0.3 0.4 0.3 0.3 0.3 0.3 0.2
0
0.4 0.4
[1] 1yqs.a 0.2 0.2 0.4 0.4 0.4 0.3 0.3 0.3 0.3 0.3 0.3 0.5 0.4
0
0.2
[1] 3pte.a 0.2 0.1 0.4 0.3 0.4 0.3 0.2 0.3 0.3 0.2 0.3 0.5 0.4 0.2
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

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
1cef.a
1ceg.a
1hvb.a
1ikg.a
1iki.a
1mpl.a
1pw1.a
1pw8.a
1pwc.a
1pwd.a
1pwg.a
1scw.a
1sde.a
1yqs.a
3pte.a
[1] 1cef.a
0
0.4 0.7 0.8 0.7 0.6 0.7 0.6 0.6 0.6 0.6 0.7 0.7 0.6 0.5
[1] 1ceg.a 0.4
0
0.6 0.7 0.6 0.5 0.6 0.5 0.5 0.5 0.5 0.6 0.6 0.6 0.3
[1] 1hvb.a 0.7 0.6
0
0.7 0.4 0.6 0.6 0.5 0.5 0.5 0.5 0.4 0.4 0.4 0.6
[1] 1ikg.a 0.8 0.7 0.7
0
0.6 0.6 0.5 0.6 0.6 0.6 0.6 0.7 0.7 0.7 0.7
[1] 1iki.a 0.7 0.6 0.4 0.6
0
0.5 0.5 0.4 0.4 0.4 0.5 0.4 0.3 0.4 0.6
[1] 1mpl.a 0.6 0.5 0.6 0.6 0.5
0
0.6 0.5 0.5 0.5 0.5 0.6 0.6 0.6 0.4
[1] 1pw1.a 0.7 0.6 0.6 0.5 0.5 0.6
0
0.5 0.5 0.5 0.5 0.6 0.6 0.6 0.6
[1] 1pw8.a 0.6 0.5 0.5 0.6 0.4 0.5 0.5
0
0.2 0.1 0.2 0.5 0.5 0.5 0.5
[1] 1pwc.a 0.6 0.5 0.5 0.6 0.4 0.5 0.5 0.2
0
0.1 0.3 0.5 0.5 0.5 0.4
[1] 1pwd.a 0.6 0.5 0.5 0.6 0.4 0.5 0.5 0.1 0.1
0
0.3 0.5 0.5 0.5 0.4
[1] 1pwg.a 0.6 0.5 0.5 0.6 0.5 0.5 0.5 0.2 0.3 0.3
0
0.5 0.5 0.5 0.5
[1] 1scw.a 0.7 0.6 0.4 0.7 0.4 0.6 0.6 0.5 0.5 0.5 0.5
0
0.4 0.5 0.6
[1] 1sde.a 0.7 0.6 0.4 0.7 0.3 0.6 0.6 0.5 0.5 0.5 0.5 0.4
0
0.4 0.6
[1] 1yqs.a 0.6 0.6 0.4 0.7 0.4 0.6 0.6 0.5 0.5 0.5 0.5 0.5 0.4
0
0.5
[1] 3pte.a 0.5 0.3 0.6 0.7 0.6 0.4 0.6 0.5 0.4 0.4 0.5 0.6 0.6 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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