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DDLB_ECOLI_1_306

D-alanine--D-alanine ligase B [D-alanine--D-alanine ligase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DDLB_ECOLI):D: ATP-grasp (142, 144, 148:151, 154, 180:183, 187, 209, 210, 215, 216, 255, 257, 259, 269, 270, 272, 275, 276, 281, 282)
15, 18, 63, 97
15, 18, 63, 97, 142, 144, 148:151, 154, 180:183, 187, 209, 210, 215, 216, 255, 257, 259, 269, 270, 272, 275, 276, 281, 282
Metals (Me):Mg

Full PDB list

1iov, 1iow, 2dln, 4c5a, 4c5b, 4c5c

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
E
1
5
V
1
8
H
6
3
K
9
7
I
1
4
2
K
1
4
4
E
1
4
8
G
1
4
9
S
1
5
0
S
1
5
1
M
1
5
4
E
1
8
0
K
1
8
1
W
1
8
2
L
1
8
3
E
1
8
7
F
2
0
9
Y
2
1
0
K
2
1
5
Y
2
1
6
R
2
5
5
D
2
5
7
M
2
5
9
L
2
6
9
E
2
7
0
N
2
7
2
P
2
7
5
G
2
7
6
S
2
8
1
L
2
8
2
[1]1iov.a adp,pob44 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1iow.a adp,phy43 . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . Mg
[1]2dln.a adp,phy43 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4c5a.a adp,ds038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4c5b.a adp,dal.dal38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4c5c.a atp.dal.dal42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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
E
1
5
V
1
8
H
6
3
K
9
7
I
1
4
2
K
1
4
4
E
1
4
8
G
1
4
9
S
1
5
0
S
1
5
1
M
1
5
4
E
1
8
0
K
1
8
1
W
1
8
2
L
1
8
3
E
1
8
7
F
2
0
9
Y
2
1
0
K
2
1
5
Y
2
1
6
R
2
5
5
D
2
5
7
M
2
5
9
L
2
6
9
E
2
7
0
N
2
7
2
P
2
7
5
G
2
7
6
S
2
8
1
L
2
8
2
[1]1iov.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1iow.a . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . Mg
[1]2dln.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4c5a.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4c5b.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4c5c.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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
1iov.a:adp,pob
1iow.a:adp,phy
2dln.a:adp,phy
4c5a.a:adp,ds0
4c5b.a:adp,dal.dal
4c5c.a:atp.dal.dal
[1] 1iov.a
0.9
0.6 0.7 0.6 0.8 0.6
[1] 1iow.a 0.1
0.1
0 0.2 0.2 0.1
[1] 2dln.a 0.4 0.2
0.4
0.2 0.3 0.1
[1] 4c5a.a 0.6 0 0.2
0
0.1 0
[1] 4c5b.a 0.5 0.2 0.2 0.3
0
0.1
[1] 4c5c.a 0.5 0.3 0.6 0.4 0.3
0.1
[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
1iov.a
1iow.a
2dln.a
4c5a.a
4c5b.a
4c5c.a
[1] 1iov.a
0
.04 .03 .04 .04 .02
[1] 1iow.a .04
0
.01 .03 .02 .02
[1] 2dln.a .03 .01
0
.03 .03 .02
[1] 4c5a.a .04 .03 .03
0
.01 .02
[1] 4c5b.a .04 .02 .03 .01
0
.01
[1] 4c5c.a .02 .02 .02 .02 .01
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

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
1iov.a
1iow.a
2dln.a
4c5a.a
4c5b.a
4c5c.a
[1] 1iov.a
0
0.3 0.3 0.4 0.4 0.3
[1] 1iow.a 0.3
0
0.2 0.4 0.4 0.3
[1] 2dln.a 0.3 0.2
0
0.4 0.4 0.3
[1] 4c5a.a 0.4 0.4 0.4
0
0.2 0.3
[1] 4c5b.a 0.4 0.4 0.4 0.2
0
0.3
[1] 4c5c.a 0.3 0.3 0.3 0.3 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
1iov.a
1iow.a
2dln.a
4c5a.a
4c5b.a
4c5c.a
[1] 1iov.a
0
0.4 0.4 0.6 0.6 0.6
[1] 1iow.a 0.4
0
0.3 0.5 0.6 0.5
[1] 2dln.a 0.4 0.3
0
0.5 0.6 0.5
[1] 4c5a.a 0.6 0.5 0.5
0
0.3 0.4
[1] 4c5b.a 0.6 0.6 0.6 0.3
0
0.2
[1] 4c5c.a 0.6 0.5 0.5 0.4 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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