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DAPDH_CORGL_1_320

Meso-diaminopimelate D-dehydrogenase [Diaminopimelate dehydrogenase family]

Composition of the binding site

Protein chains monomer
A1 (DAPDH_CORGL):90, 119, 120, 144, 149, 152, 169, 195, 244, 27090, 119, 120, 144, 149:152, 169, 195, 244, 270
Cofactors (cF):nap/ndp

Full PDB list

1dap, 1f06, 2dap, 3dap, 5loa, 5loc (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
D
9
0
W
1
1
9
D
1
2
0
W
1
4
4
S
1
4
9
Q
1
5
0
G
1
5
1
H
1
5
2
T
1
6
9
R
1
9
5
H
2
4
4
N
2
7
0
[1]1dap.b none . . . . . . . . . . . . ndp
[1]1f06.b 2np13 . . . . . . . . . . . . ndp
[1]2dap.a api13 . . . . . . . . . . . .
[1]3dap.b da314 . . . . . . . . . . . . ndp
[1]5loa.b none . . . . . L . . I M N . nap

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 cF
D
9
0
W
1
1
9
D
1
2
0
W
1
4
4
S
1
4
9
Q
1
5
0
G
1
5
1
H
1
5
2
T
1
6
9
R
1
9
5
H
2
4
4
N
2
7
0
[1]1dap.b . . . . . . . . . . . . ndp
[1]1f06.b . . . . . . . . . . . . ndp
[1]2dap.a . . . . . . . . . . . .
[1]3dap.b . . . . . . . . . . . . ndp
[1]5loa.b . . . . . L . . I M N . nap

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
1dap.b is apo
1f06.b:2np
2dap.a:api
3dap.b:da3
5loa.b is apo
[1] 1dap.b
-
0.2 0.1 0.3 -
[1] 1f06.b -
0.1
0.1 0 -
[1] 2dap.a - 0.5
0.1
0.2 -
[1] 3dap.b - 0.3 0.1
0.1
-
[1] 5loa.b - 0.1 0 0.3
-
[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
1dap.b
1f06.b
2dap.a
3dap.b
5loa.b
[1] 1dap.b
0
.02 .04 .03 .03
[1] 1f06.b .02
0
.04 .02 .03
[1] 2dap.a .04 .04
0
.05 .05
[1] 3dap.b .03 .02 .05
0
.05
[1] 5loa.b .03 .03 .05 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1dap.b
1f06.b
2dap.a
3dap.b
5loa.b
[1] 1dap.b
0
0.2 0.8 0.2 0.3
[1] 1f06.b 0.2
0
0.8 0.2 0.3
[1] 2dap.a 0.8 0.8
0
0.9 0.9
[1] 3dap.b 0.2 0.2 0.9
0
0.3
[1] 5loa.b 0.3 0.3 0.9 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

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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
1dap.b
1f06.b
2dap.a
3dap.b
5loa.b
[1] 1dap.b
0
0.4 1.2 0.4 0.6
[1] 1f06.b 0.4
0
1.2 0.4 0.6
[1] 2dap.a 1.2 1.2
0
1.1 1.1
[1] 3dap.b 0.4 0.4 1.1
0
0.6
[1] 5loa.b 0.6 0.6 1.1 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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