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DPAL_ECOLI_1_398

Diaminopropionate ammonia-lyase [Diaminopropionate ammonia-lyase family]

Composition of the binding site

Protein chains monomer
A1 (DPAL_ECOLI):76, 77, 119, 120, 122, 123, 168, 189, 230:236, 288:290, 339, 376, 37776, 77, 119, 120, 122, 123, 168, 189, 230:236, 288:290, 339, 376, 377

Full PDB list

4d9g, 4d9i, 4d9k, 4d9m, 4d9n

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
7
6
K
7
7
T
1
1
9
D
1
2
0
N
1
2
2
H
1
2
3
Y
1
6
8
D
1
8
9
Q
2
3
0
A
2
3
1
G
2
3
2
V
2
3
3
G
2
3
4
A
2
3
5
M
2
3
6
G
2
8
8
L
2
8
9
A
2
9
0
S
3
3
9
T
3
7
6
E
3
7
7
[1]4d9g.a none . * . . . . . . . . . . . . * . . . . . .
[1]4d9i.a none . * . . . . . . . . . . . . . . . . . . .
[1]4d9n.a dsn7 . * . . . . . . . . . . . . . . . . . . .
[2]4d9k.d none . . . . . . . . . . . . . . . - - - . . .
[2]4d9m.a 0jo21 . . . . . . . . . . . . . . . . . . . . .

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
F
7
6
K
7
7
T
1
1
9
D
1
2
0
N
1
2
2
H
1
2
3
Y
1
6
8
D
1
8
9
Q
2
3
0
A
2
3
1
G
2
3
2
V
2
3
3
G
2
3
4
A
2
3
5
M
2
3
6
G
2
8
8
L
2
8
9
A
2
9
0
S
3
3
9
T
3
7
6
E
3
7
7
[1]4d9g.a . it1 . . . . . . . . . . . . * . . . . . .
[1]4d9i.a . it1 . . . . . . . . . . . . . . . . . . .
[1]4d9n.a . it1 . . . . . . . . . . . . . . . . . . .
[2]4d9k.d . . . . . . . . . . . . . . . - - - . . .
[2]4d9m.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
4d9g.a is apo
4d9i.a is apo
4d9n.a:dsn
4d9k.d is apo
4d9m.a:0jo
[1] 4d9g.a
-
- 0 - 11
[1] 4d9i.a -
-
0 - 11
[1] 4d9n.a - -
0
- 11
[2] 4d9k.d - - 0.2
-
1.0
[2] 4d9m.a - - 0.1 -
0
[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
4d9g.a
4d9i.a
4d9n.a
4d9k.d
4d9m.a
[1] 4d9g.a
0
.02 .02 .52 .52
[1] 4d9i.a .02
0
.02 .54 .53
[1] 4d9n.a .02 .02
0
.53 .53
[2] 4d9k.d .52 .54 .53
0
.06
[2] 4d9m.a .52 .53 .53 .06
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
4d9g.a
4d9i.a
4d9n.a
4d9k.d
4d9m.a
[1] 4d9g.a
0
0.2 0.2 0.7 0.5
[1] 4d9i.a 0.2
0
0.2 0.7 0.5
[1] 4d9n.a 0.2 0.2
0
0.6 0.4
[2] 4d9k.d 0.7 0.7 0.6
0
0.7
[2] 4d9m.a 0.5 0.5 0.4 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue 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
4d9g.a
4d9i.a
4d9n.a
4d9k.d
4d9m.a
[1] 4d9g.a
0
0.2 0.6 0.9 0.5
[1] 4d9i.a 0.2
0
0.6 0.9 0.5
[1] 4d9n.a 0.6 0.6
0
0.8 0.5
[2] 4d9k.d 0.9 0.9 0.8
0
0.8
[2] 4d9m.a 0.5 0.5 0.5 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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