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DAPE_NEIMB_1_381

Succinyl-diaminopimelate desuccinylase [Peptidase M20A family. DapE subfamily]

Composition of the binding site

Protein chains monomer
A1 (DAPE_NEIMB):68, 101, 135, 136, 164, 179, 325, 326, 346, 349, 35068, 101, 135, 136, 164, 179, 325, 326, 346, 349, 350
Metals (Me):Zn

Full PDB list

1vgy, 4o23, 4ppz, 4pqa, 5uej (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
6
8
D
1
0
1
E
1
3
5
E
1
3
6
E
1
6
4
R
1
7
9
G
3
2
5
T
3
2
6
N
3
4
6
I
3
4
9
H
3
5
0
[1]4pqa.a x8z14 . . . . . . . . . . . Zn
[1]5uej.a none . . . . . . . . . . . Zn

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 Me
H
6
8
D
1
0
1
E
1
3
5
E
1
3
6
E
1
6
4
R
1
7
9
G
3
2
5
T
3
2
6
N
3
4
6
I
3
4
9
H
3
5
0
[1]4pqa.a . . . . . . . . . . . Zn
[1]5uej.a . . . . . . . . . . . Zn

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
4pqa.a:x8z
5uej.a is apo
[1] 4pqa.a
0
-
[1] 5uej.a 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
4pqa.a
5uej.a
[1] 4pqa.a
0
0
[1] 5uej.a 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.1 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
4pqa.a
5uej.a
[1] 4pqa.a
0
0.2
[1] 5uej.a 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
4pqa.a
5uej.a
[1] 4pqa.a
0
0.3
[1] 5uej.a 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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