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DAPD_YERPE_1_270

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [Transferase hexapeptide repeat family]

Composition of the binding site

Protein chains homodimer
A1 (DAPD_YERPE):104, 124, 139, 141, 270104, 124, 139, 141, 270
A2 (DAPD_YERPE):67, 112, 129, 148, 166:16967, 112, 129, 148, 166:169

Full PDB list

1kgq, 1kgt, 1tdt, 2tdt, 3gos, 3tdt (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
R
1
0
4
M
1
2
4
M
1
3
9
D
1
4
1
L
2
7
0
F
6
7
R
1
1
2
N
1
2
9
S
1
4
8
G
1
6
6
V
1
6
7
L
1
6
8
E
1
6
9
[1]1kgt.a pml11 . . . . . . . . . . . . .
[1]2tdt.a npi12 . . . . . . . . . . . . .
[1]3gos.b none . . . . . . . . . . . . .
[1]3tdt.a 26p13 . . . . . . . . . . . . .

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 A2
R
1
0
4
M
1
2
4
M
1
3
9
D
1
4
1
L
2
7
0
F
6
7
R
1
1
2
N
1
2
9
S
1
4
8
G
1
6
6
V
1
6
7
L
1
6
8
E
1
6
9
[1]1kgt.a . . . . . . . . . . . . .
[1]2tdt.a . . . . . . . . . . . . .
[1]3gos.b . . . . . . . . . . . . .
[1]3tdt.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
1kgt.a:pml
2tdt.a:npi
3gos.b is apo
3tdt.a:26p
[1] 1kgt.a
0
0.2 - 0.1
[1] 2tdt.a 0
0
- 0
[1] 3gos.b 0 0
-
0
[1] 3tdt.a 0 0 -
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
1kgt.a
2tdt.a
3gos.b
3tdt.a
[1] 1kgt.a
0
.02 .02 .02
[1] 2tdt.a .02
0
0 0
[1] 3gos.b .02 0
0
0
[1] 3tdt.a .02 0 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1kgt.a
2tdt.a
3gos.b
3tdt.a
[1] 1kgt.a
0
0.2 6.9 0.2
[1] 2tdt.a 0.2
0
6.9 0.1
[1] 3gos.b 6.9 6.9
0
6.9
[1] 3tdt.a 0.2 0.1 6.9
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
1kgt.a
2tdt.a
3gos.b
3tdt.a
[1] 1kgt.a
0
0.2 6.4 0.3
[1] 2tdt.a 0.2
0
6.5 0.1
[1] 3gos.b 6.4 6.5
0
6.5
[1] 3tdt.a 0.3 0.1 6.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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