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DAC_ACTSP_50_523

D-alanyl-D-alanine carboxypeptidase [Peptidase S13 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DAC_ACTSP):R: Absent in class-A beta-lactamases (188, 191, 196)
97, 98, 101, 346, 347, 349, 396:398, 400, 442, 459:464
97, 98, 101, 188, 191, 196, 346, 347, 349, 396:398, 400, 442, 459:464

Full PDB list

1w79, 1w8q, 1w8y, 2vgj, 2vgk, 2wke, 2xdm, 2xk1, 2xln, 2y4a, 2y55, 2y59, 3zcz, 3zvt, 3zvw, 4b4x, 4b4z, 4ben (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
9
7
S
9
8
K
1
0
1
W
1
8
8
D
1
9
1
Y
1
9
6
S
3
4
7
N
3
4
9
S
3
9
6
G
3
9
7
L
3
9
8
R
4
0
0
T
4
4
2
K
4
5
9
T
4
6
0
G
4
6
1
T
4
6
2
M
4
6
3
S
4
6
4
[1]1w79.a none . . . . . . . . . . . . . . . . . . .
[1]1w8y.c ncf21 . * . . . . . . . . . . . . . . . . .
[1]2vgj.a rec25 . * . . . . . . . . . . . . . . . . .
[1]2vgk.a rez17 . . . . . . . . . . . . . . . . . . .
[1]2wke.b biy13 . * . . . . . . . . . . . . . . . . .
[1]2xdm.b bo817 . * . . . . . . . . . . . . . . . . .
[1]2xk1.b ewb21 . * . . . . . . . . . . . . . . . . .
[1]2xln.a ewa18 . * . . . . . . . . . . . . . . . . .
[1]2y4a.b bh612 . . . . . . * . . . . . . . . . . . .
[1]2y55.b fp512 . * . . . . . . . . . . . . . . . . .
[1]2y59.b za314 . * . . . . . . . . . . . . . . . . .
[1]3zcz.a tfr20 . * . . . . . . . . . . . . . . . . .
[1]3zvt.c b0715 . * . . . . . . . . . . . . . . . . .
[1]3zvw.b 33d,fp519 . . . . . . * . . . . . . . . . . . .
[1]4b4x.b hqz10 . * . . . . . . . . . . . . . . . . .
[1]4b4z.b bsf13 . * . . . . . . . . . . . . . . . . .
[1]4ben.a im215 . * . . . . . . . . . . . . . . . . .

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
A
9
7
S
9
8
K
1
0
1
W
1
8
8
D
1
9
1
Y
1
9
6
F
3
4
6
S
3
4
7
N
3
4
9
S
3
9
6
G
3
9
7
L
3
9
8
R
4
0
0
T
4
4
2
K
4
5
9
T
4
6
0
G
4
6
1
T
4
6
2
M
4
6
3
S
4
6
4
[1]1w79.a . * . . . . . * . . . . . . . . . . . .
[1]1w8y.c . * . . . . . * . . . . . . . . . . . .
[1]2vgj.a . * . . . . . * . . . . . . . . . . . .
[1]2vgk.a . * . . . . . * . . . . . . . . . . . .
[1]2wke.b . * . . . . . * . . . . . . . . . . . .
[1]2xdm.b . * . . . . . * . . . . . . . . . . . .
[1]2xk1.b . * . . . . . * . . . . . . . . . . . .
[1]2xln.a . * . . . . . * . . . . . . . . . . . .
[1]2y4a.b . . . . . . . * . . . . . . . . . . . .
[1]2y55.b . * . . . . . * . . . . . . . . . . . .
[1]2y59.b . * . . . . . * . . . . . . . . . . . .
[1]3zcz.a . * . . . . . * . . . . . . . . . . . .
[1]3zvt.c . * . . . . . . . . . . . . . . . . . .
[1]3zvw.b . * . . . . . * . . . . . . . . . . . .
[1]4b4x.b . * . . . . . * . . . . . . . . . . . .
[1]4b4z.b . * . . . . . * . . . . . . . . . . . .
[1]4ben.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
1w79.a is apo
1w8y.c:ncf
2vgj.a:rec
2vgk.a:rez
2wke.b:biy
2xdm.b:bo8
2xk1.b:ewb
2xln.a:ewa
2y4a.b:bh6
2y55.b:fp5
2y59.b:za3
3zcz.a:tfr
3zvt.c:b07
3zvw.b:33d,fp5
4b4x.b:hqz
4b4z.b:bsf
4ben.a:im2
[1] 1w79.a
-
1.1 0.7 0 0.4 0.6 0.6 0.6 1.1 1.4 1.2 0.4 1.4 1.3 0.5 1.0 0.5
[1] 1w8y.c -
0.9
0.8 0.2 0.5 0.6 0.6 0.6 1.1 1.6 1.0 0.7 1.3 1.7 0.6 1.1 0.8
[1] 2vgj.a - 1.2
0.7
0.1 0.4 0.6 0.7 0.6 1.0 1.1 0.8 0.6 0.9 1.3 0.7 0.9 0.8
[1] 2vgk.a - 0.7 0.7
0.1
0.4 0.6 0.6 0.6 1.1 1.1 0.8 0.4 0.9 1.4 0.4 0.9 0.4
[1] 2wke.b - 1.0 1.0 0.7
0.6
0.7 0.6 0.8 0.9 1.1 1.1 1.1 0.9 1.1 0.6 0.8 0.9
[1] 2xdm.b - 0.7 0.8 0.4 0.4
0.6
0.6 0.6 1.1 1.3 0.9 0.8 1.3 1.7 0.6 1.1 0.5
[1] 2xk1.b - 0.4 0.8 0.7 0.6 0.6
0.4
0.4 1.1 1.4 1.0 0.9 1.0 2.1 0.6 1.0 0.5
[1] 2xln.a - 0.8 0.4 0 0.5 0.4 0.4
0.4
1.2 1.6 1.4 0.5 1.2 2.0 0.7 1.5 0.6
[1] 2y4a.b - 0.7 1.0 0.7 0.3 0.5 0.4 0.3
1.3
1.4 1.2 0.7 1.4 1.2 0.1 1.3 0.4
[1] 2y55.b - 0.5 0.5 0.6 0.1 0.2 0.1 0.1 1.4
1.2
1.2 0.5 1.6 1.2 0.1 1.4 0.4
[1] 2y59.b - 0.6 0.8 0.4 0.3 0.1 0.3 0.3 1.7 1.6
1.4
0.5 1.6 1.6 0.1 1.6 0.5
[1] 3zcz.a - 1.0 0.8 0.1 0.6 0.6 0.6 0.6 1.1 1.4 1.0
0.6
1.3 1.5 0.7 1.0 0.7
[1] 3zvt.c - 0.7 1.4 0.7 0.3 0.6 0.3 0.3 1.3 1.3 1.3 1.1
1.1
1.4 0.2 1.1 0.4
[1] 3zvw.b - 0.6 0.7 0.6 0.1 0.2 0.2 0.1 1.6 1.6 1.2 0.6 1.6
1.2
0.1 1.5 0.2
[1] 4b4x.b - 1.1 1.2 0.6 0.5 0.7 0.6 0.8 0.9 1.2 0.8 0.9 0.8 1.5
0.6
0.8 0.9
[1] 4b4z.b - 0.7 0.8 0.7 0.1 0.3 0.4 0.4 1.4 1.2 1.2 0.9 1.6 1.2 0.2
1.2
0.5
[1] 4ben.a - 1.0 0.6 0 0.4 0.6 0.6 0.8 1.1 1.4 1.4 0.6 1.4 1.6 0.6 1.0
0.8
[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
1w79.a
1w8y.c
2vgj.a
2vgk.a
2wke.b
2xdm.b
2xk1.b
2xln.a
2y4a.b
2y55.b
2y59.b
3zcz.a
3zvt.c
3zvw.b
4b4x.b
4b4z.b
4ben.a
[1] 1w79.a
0
.06 .07 .05 .06 .09 .15 .07 .09 .07 .06 .05 .11 .07 .10 .08 .04
[1] 1w8y.c .06
0
.08 .07 .08 .05 .10 .05 .10 .10 .09 .04 .13 .11 .06 .10 .07
[1] 2vgj.a .07 .08
0
.07 .09 .08 .14 .10 .11 .11 .09 .06 .12 .10 .08 .12 .08
[1] 2vgk.a .05 .07 .07
0
.09 .05 .12 .08 .09 .07 .07 .06 .11 .07 .11 .09 .06
[1] 2wke.b .06 .08 .09 .09
0
.11 .14 .12 .04 .03 .05 .09 .08 .03 .06 .04 .08
[1] 2xdm.b .09 .05 .08 .05 .11
0
.08 .07 .10 .10 .07 .05 .11 .09 .11 .10 .10
[1] 2xk1.b .15 .10 .14 .12 .14 .08
0
.10 .13 .12 .13 .11 .12 .12 .08 .12 .14
[1] 2xln.a .07 .05 .10 .08 .12 .07 .10
0
.10 .10 .09 .07 .12 .11 .10 .10 .07
[1] 2y4a.b .09 .10 .11 .09 .04 .10 .13 .10
0
.02 .02 .10 .06 .03 .09 .02 .11
[1] 2y55.b .07 .10 .11 .07 .03 .10 .12 .10 .02
0
.03 .10 .06 .01 .08 .01 .09
[1] 2y59.b .06 .09 .09 .07 .05 .07 .13 .09 .02 .03
0
.08 .07 .03 .10 .04 .10
[1] 3zcz.a .05 .04 .06 .06 .09 .05 .11 .07 .10 .10 .08
0
.10 .10 .09 .10 .05
[1] 3zvt.c .11 .13 .12 .11 .08 .11 .12 .12 .06 .06 .07 .10
0
.06 .11 .05 .12
[1] 3zvw.b .07 .11 .10 .07 .03 .09 .12 .11 .03 .01 .03 .10 .06
0
.09 .02 .11
[1] 4b4x.b .10 .06 .08 .11 .06 .11 .08 .10 .09 .08 .10 .09 .11 .09
0
.09 .10
[1] 4b4z.b .08 .10 .12 .09 .04 .10 .12 .10 .02 .01 .04 .10 .05 .02 .09
0
.11
[1] 4ben.a .04 .07 .08 .06 .08 .10 .14 .07 .11 .09 .10 .05 .12 .11 .10 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1w79.a
1w8y.c
2vgj.a
2vgk.a
2wke.b
2xdm.b
2xk1.b
2xln.a
2y4a.b
2y55.b
2y59.b
3zcz.a
3zvt.c
3zvw.b
4b4x.b
4b4z.b
4ben.a
[1] 1w79.a
0
0.4 0.3 0.3 0.2 0.3 0.5 0.4 0.3 0.3 0.3 0.2 0.4 0.2 0.5 0.3 0.2
[1] 1w8y.c 0.4
0
0.4 0.5 0.4 0.4 0.5 0.4 0.4 0.5 0.5 0.4 0.5 0.4 0.5 0.4 0.4
[1] 2vgj.a 0.3 0.4
0
0.3 0.3 0.3 0.4 0.4 0.4 0.4 0.4 0.3 0.4 0.3 0.5 0.4 0.3
[1] 2vgk.a 0.3 0.5 0.3
0
0.3 0.3 0.4 0.4 0.4 0.4 0.4 0.3 0.4 0.3 0.4 0.4 0.3
[1] 2wke.b 0.2 0.4 0.3 0.3
0
0.3 0.5 0.4 0.2 0.2 0.3 0.3 0.3 0.2 0.5 0.2 0.2
[1] 2xdm.b 0.3 0.4 0.3 0.3 0.3
0
0.3 0.3 0.3 0.3 0.3 0.2 0.4 0.3 0.3 0.3 0.2
[1] 2xk1.b 0.5 0.5 0.4 0.4 0.5 0.3
0
0.3 0.5 0.5 0.5 0.3 0.5 0.5 0.3 0.5 0.4
[1] 2xln.a 0.4 0.4 0.4 0.4 0.4 0.3 0.3
0
0.4 0.5 0.5 0.2 0.5 0.4 0.4 0.5 0.3
[1] 2y4a.b 0.3 0.4 0.4 0.4 0.2 0.3 0.5 0.4
0
0.2 0.2 0.3 0.3 0.2 0.5 0.2 0.2
[1] 2y55.b 0.3 0.5 0.4 0.4 0.2 0.3 0.5 0.5 0.2
0
0.2 0.3 0.3 0.2 0.5 0.2 0.3
[1] 2y59.b 0.3 0.5 0.4 0.4 0.3 0.3 0.5 0.5 0.2 0.2
0
0.4 0.3 0.2 0.6 0.2 0.3
[1] 3zcz.a 0.2 0.4 0.3 0.3 0.3 0.2 0.3 0.2 0.3 0.3 0.4
0
0.4 0.3 0.4 0.4 0.2
[1] 3zvt.c 0.4 0.5 0.4 0.4 0.3 0.4 0.5 0.5 0.3 0.3 0.3 0.4
0
0.3 0.5 0.3 0.3
[1] 3zvw.b 0.2 0.4 0.3 0.3 0.2 0.3 0.5 0.4 0.2 0.2 0.2 0.3 0.3
0
0.5 0.2 0.2
[1] 4b4x.b 0.5 0.5 0.5 0.4 0.5 0.3 0.3 0.4 0.5 0.5 0.6 0.4 0.5 0.5
0
0.6 0.4
[1] 4b4z.b 0.3 0.4 0.4 0.4 0.2 0.3 0.5 0.5 0.2 0.2 0.2 0.4 0.3 0.2 0.6
0
0.3
[1] 4ben.a 0.2 0.4 0.3 0.3 0.2 0.2 0.4 0.3 0.2 0.3 0.3 0.2 0.3 0.2 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

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
1w79.a
1w8y.c
2vgj.a
2vgk.a
2wke.b
2xdm.b
2xk1.b
2xln.a
2y4a.b
2y55.b
2y59.b
3zcz.a
3zvt.c
3zvw.b
4b4x.b
4b4z.b
4ben.a
[1] 1w79.a
0
0.6 0.3 0.4 0.5 0.5 0.7 0.6 0.6 0.6 0.6 0.5 0.7 0.5 0.8 0.6 0.6
[1] 1w8y.c 0.6
0
0.6 0.7 0.6 0.6 0.6 0.5 0.6 0.6 0.6 0.6 0.8 0.6 0.8 0.6 0.7
[1] 2vgj.a 0.3 0.6
0
0.3 0.5 0.4 0.6 0.6 0.6 0.6 0.6 0.5 0.7 0.5 0.8 0.6 0.6
[1] 2vgk.a 0.4 0.7 0.3
0
0.6 0.5 0.6 0.6 0.6 0.6 0.6 0.5 0.8 0.6 0.7 0.7 0.6
[1] 2wke.b 0.5 0.6 0.5 0.6
0
0.3 0.6 0.6 0.3 0.4 0.3 0.5 0.6 0.3 0.6 0.4 0.6
[1] 2xdm.b 0.5 0.6 0.4 0.5 0.3
0
0.5 0.6 0.4 0.5 0.4 0.4 0.6 0.4 0.6 0.5 0.6
[1] 2xk1.b 0.7 0.6 0.6 0.6 0.6 0.5
0
0.6 0.7 0.6 0.7 0.6 0.7 0.6 0.6 0.7 0.7
[1] 2xln.a 0.6 0.5 0.6 0.6 0.6 0.6 0.6
0
0.7 0.7 0.7 0.5 0.8 0.7 0.7 0.7 0.7
[1] 2y4a.b 0.6 0.6 0.6 0.6 0.3 0.4 0.7 0.7
0
0.3 0.2 0.6 0.5 0.2 0.7 0.3 0.6
[1] 2y55.b 0.6 0.6 0.6 0.6 0.4 0.5 0.6 0.7 0.3
0
0.3 0.6 0.5 0.2 0.7 0.3 0.6
[1] 2y59.b 0.6 0.6 0.6 0.6 0.3 0.4 0.7 0.7 0.2 0.3
0
0.6 0.5 0.2 0.7 0.3 0.6
[1] 3zcz.a 0.5 0.6 0.5 0.5 0.5 0.4 0.6 0.5 0.6 0.6 0.6
0
0.7 0.6 0.7 0.6 0.5
[1] 3zvt.c 0.7 0.8 0.7 0.8 0.6 0.6 0.7 0.8 0.5 0.5 0.5 0.7
0
0.5 0.8 0.5 0.6
[1] 3zvw.b 0.5 0.6 0.5 0.6 0.3 0.4 0.6 0.7 0.2 0.2 0.2 0.6 0.5
0
0.7 0.2 0.6
[1] 4b4x.b 0.8 0.8 0.8 0.7 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.7 0.8 0.7
0
0.7 0.8
[1] 4b4z.b 0.6 0.6 0.6 0.7 0.4 0.5 0.7 0.7 0.3 0.3 0.3 0.6 0.5 0.2 0.7
0
0.6
[1] 4ben.a 0.6 0.7 0.6 0.6 0.6 0.6 0.7 0.7 0.6 0.6 0.6 0.5 0.6 0.6 0.8 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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