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DAPF_HAEIN_1_274

Diaminopimelate epimerase [Diaminopimelate epimerase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DAPF_HAEIN):R: Substrate binding (74, 75)
R: Substrate binding (208, 209)
R: Substrate binding (218, 219)
11, 13, 44, 64, 70:73, 157, 190, 217
11, 13, 44, 64, 70:75, 157, 190, 208, 209, 217:219

Full PDB list

1bwz, 1gqz, 2gke, 2gkj, 2q9h, 2q9j (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
N
1
1
F
1
3
Q
4
4
N
6
4
V
7
0
Q
7
2
C
7
3
G
7
4
N
7
5
N
1
5
7
N
1
9
0
E
2
0
8
R
2
0
9
C
2
1
7
G
2
1
8
S
2
1
9
[1]2gke.a zdp14 . . . . . . * . . . . . . . . .
[1]2gkj.a zdr14 . . . . . . . . . . . . . * . .
[1]2q9h.a none . . . . . . S . . . . . . . . .
[1]2q9j.a none . . . . . . * . . . . . . S . .
[2]1gqz.a none . . . . . . . . . . . . . . . .

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
N
1
1
F
1
3
Q
4
4
N
6
4
V
7
0
S
7
1
Q
7
2
C
7
3
G
7
4
N
7
5
N
1
5
7
N
1
9
0
E
2
0
8
R
2
0
9
C
2
1
7
G
2
1
8
S
2
1
9
[1]2gke.a . . . . . . . * . . . . . . . . .
[1]2gkj.a . . . . . . . * . . . . . . * . .
[1]2q9h.a . . . . . . . S . . . . . . . . .
[1]2q9j.a . . . . . . . * . . . . . . S . .
[2]1gqz.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
2gke.a:zdp
2gkj.a:zdr
2q9h.a is apo
2q9j.a is apo
1gqz.a is apo
[1] 2gke.a
0.4
0.8 - - -
[1] 2gkj.a 0.7
0.4
- - -
[1] 2q9h.a 0.6 0.9
-
- -
[1] 2q9j.a 1.1 1.2 -
-
-
[2] 1gqz.a 8.1 8.0 - -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
2gke.a
2gkj.a
2q9h.a
2q9j.a
1gqz.a
[1] 2gke.a
0
.04 .09 .11 .48
[1] 2gkj.a .04
0
.08 .12 .44
[1] 2q9h.a .09 .08
0
.09 .45
[1] 2q9j.a .11 .12 .09
0
.47
[2] 1gqz.a .48 .44 .45 .47
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.8 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
2gke.a
2gkj.a
2q9h.a
2q9j.a
1gqz.a
[1] 2gke.a
0
0.1 3.9 4.5 3.9
[1] 2gkj.a 0.1
0
3.8 4.4 3.8
[1] 2q9h.a 3.9 3.8
0
0.9 1.5
[1] 2q9j.a 4.5 4.4 0.9
0
1.5
[2] 1gqz.a 3.9 3.8 1.5 1.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.5 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
2gke.a
2gkj.a
2q9h.a
2q9j.a
1gqz.a
[1] 2gke.a
0
0.2 4.1 4.7 4.4
[1] 2gkj.a 0.2
0
4.0 4.7 4.3
[1] 2q9h.a 4.1 4.0
0
1.0 1.7
[1] 2q9j.a 4.7 4.7 1.0
0
1.8
[2] 1gqz.a 4.4 4.3 1.7 1.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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