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DAPDH_URETH_1_326

Meso-diaminopimelate D-dehydrogenase [Diaminopimelate dehydrogenase family]

Composition of the binding site

Protein chains monomer
A1 (DAPDH_URETH):123, 124, 148, 153, 156, 173, 199, 249, 276123, 124, 148, 153, 156, 173, 199, 249, 276
Cofactors (cF):nap

Full PDB list

3wyb, 3wyc, 5gz1, 5gz3, 5gz6 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 cF
W
1
2
3
D
1
2
4
W
1
4
8
S
1
5
3
H
1
5
6
T
1
7
3
R
1
9
9
H
2
4
9
[1]3wyb.b none . . . . . . . .
[1]3wyc.a nes14 . . . . . . . . nap
[1]5gz1.a none . . . . - I M N

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
W
1
2
3
D
1
2
4
W
1
4
8
S
1
5
3
H
1
5
6
T
1
7
3
R
1
9
9
H
2
4
9
N
2
7
6
[1]3wyb.b . . . . . . . . .
[1]3wyc.a . . . . . . . . . nap
[1]5gz1.a . . * . - I M N .

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
3wyb.b is apo
3wyc.a:nes
5gz1.a is apo
[1] 3wyb.b
-
0 -
[1] 3wyc.a -
0
-
[1] 5gz1.a - 1.4
-
[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
3wyb.b
3wyc.a
5gz1.a
[1] 3wyb.b
0
0 .12
[1] 3wyc.a 0
0
.12
[1] 5gz1.a .12 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3wyb.b
3wyc.a
5gz1.a
[1] 3wyb.b
0
0.2 0.3
[1] 3wyc.a 0.2
0
0.4
[1] 5gz1.a 0.3 0.4
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

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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
3wyb.b
3wyc.a
5gz1.a
[1] 3wyb.b
0
0.4 1.0
[1] 3wyc.a 0.4
0
1.0
[1] 5gz1.a 1.0 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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