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DACC_ECOLI_27_378

D-alanyl-D-alanine carboxypeptidase DacC [Peptidase S11 family]

Composition of the binding site

Protein chains monomer
A1 (DACC_ECOLI):65, 66, 106:109, 112, 132, 134, 174, 175, 220, 236:239, 244, 27065, 66, 106:109, 112, 132, 134, 174, 175, 220, 236:239, 244, 270

Full PDB list

3it9, 3ita, 3itb

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
6
5
S
6
6
R
1
0
6
G
1
0
7
S
1
0
8
S
1
0
9
S
1
3
2
N
1
3
4
G
1
7
4
L
1
7
5
R
2
2
0
T
2
3
6
G
2
3
7
T
2
3
8
R
2
7
0
[1]3it9.c none . . . . . . . . . . . . . . .
[1]3ita.a aix24 . * . . . . . . . . . . . . .
[1]3itb.c amvAfgaKdal.dal54 . . . . . . . . . . . . . . .

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

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PDB.ch
A1
A
6
5
S
6
6
R
1
0
6
G
1
0
7
S
1
0
8
S
1
0
9
F
1
1
2
S
1
3
2
N
1
3
4
G
1
7
4
L
1
7
5
R
2
2
0
T
2
3
6
G
2
3
7
T
2
3
8
T
2
3
9
Y
2
4
4
R
2
7
0
[1]3it9.c . . . . . . . . . . . . . . * . . .
[1]3ita.a . * . . . . . . . . . . . . . . . .
[1]3itb.c . . . . . . . . . . . . . . * . . .

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
3it9.c is apo
3ita.a:aix
3itb.c:amvAfgaKdal.dal
[1] 3it9.c
-
2.0 0.5
[1] 3ita.a -
0.6
0.8
[1] 3itb.c - 1.5
0
[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
3it9.c
3ita.a
3itb.c
[1] 3it9.c
0
.16 .07
[1] 3ita.a .16
0
.12
[1] 3itb.c .07 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
3it9.c
3ita.a
3itb.c
[1] 3it9.c
0
1.4 0.7
[1] 3ita.a 1.4
0
1.2
[1] 3itb.c 0.7 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
3it9.c
3ita.a
3itb.c
[1] 3it9.c
0
2.3 1.8
[1] 3ita.a 2.3
0
1.7
[1] 3itb.c 1.8 1.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

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