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COBD_SALTY_1_364

Threonine-phosphate decarboxylase [Class-II pyridoxal-phosphate-dependent aminotransferase family]

Composition of the binding site

Protein chains monomer
A1 (COBD_SALTY):8, 9, 31, 32, 84:86, 89, 108, 111, 153, 157, 185, 187, 188, 213, 215, 216, 224, 323, 328, 3378, 9, 31, 32, 84:86, 89, 108, 111, 153, 157, 185, 187, 188, 213, 215, 216, 224, 323, 328, 337

Full PDB list

1lc5, 1lc7, 1lc8, 1lkc

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
8
G
9
A
3
1
N
3
2
G
8
4
E
8
5
T
8
6
I
8
9
F
1
0
8
C
1
5
3
N
1
5
7
D
1
8
5
A
1
8
7
F
1
8
8
S
2
1
3
T
2
1
5
K
2
1
6
R
2
2
4
R
3
2
3
Y
3
2
8
R
3
3
7
[1]1lc5.a none . . . . . . . . . . . . . . . . . . . . .
[1]1lc7.a tpo12 . . . . . . . . . . . . . . . . . . . . .
[1]1lc8.a 33p24 . . . . . . . . . . . . . . . . . . . . .
[1]1lkc.a plp15 . . . . . . . . . . . . . . . . * . . . .

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
H
8
G
9
A
3
1
N
3
2
G
8
4
E
8
5
T
8
6
I
8
9
F
1
0
8
Y
1
1
1
C
1
5
3
N
1
5
7
D
1
8
5
A
1
8
7
F
1
8
8
S
2
1
3
T
2
1
5
K
2
1
6
R
2
2
4
R
3
2
3
Y
3
2
8
R
3
3
7
[1]1lc5.a . . . . . . . . . . . . . . . . . * . . . .
[1]1lc7.a . . . . . . . . . . . . . . . . . . . . . .
[1]1lc8.a . . . . . . . . . . . . . . . . . . . . . .
[1]1lkc.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
1lc5.a is apo
1lc7.a:tpo
1lc8.a:33p
1lkc.a:plp
[1] 1lc5.a
-
0.3 0.2 1.0
[1] 1lc7.a -
0
0.1 0.7
[1] 1lc8.a - 0.3
0.1
0.5
[1] 1lkc.a - 0.1 0.6
0.6
[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
1lc5.a
1lc7.a
1lc8.a
1lkc.a
[1] 1lc5.a
0
.03 .03 .03
[1] 1lc7.a .03
0
.02 .03
[1] 1lc8.a .03 .02
0
.03
[1] 1lkc.a .03 .03 .03
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
1lc5.a
1lc7.a
1lc8.a
1lkc.a
[1] 1lc5.a
0
0.2 0.2 0.3
[1] 1lc7.a 0.2
0
0.2 0.3
[1] 1lc8.a 0.2 0.2
0
0.3
[1] 1lkc.a 0.3 0.3 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1lc5.a
1lc7.a
1lc8.a
1lkc.a
[1] 1lc5.a
0
0.4 0.4 0.7
[1] 1lc7.a 0.4
0
0.5 0.8
[1] 1lc8.a 0.4 0.5
0
0.7
[1] 1lkc.a 0.7 0.8 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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