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DAPAT_ARATH_36_461

LL-diaminopimelate aminotransferase, chloroplastic [Class-I pyridoxal-phosphate-dependent aminotransferase family. LL-diaminopimelate aminotransferase subfamily]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (DAPAT_ARATH):R: Pyridoxal phosphate binding (163, 164)
R: Pyridoxal phosphate binding (302, 304)
72, 74, 98, 99, 162, 167, 187, 190, 240, 244, 272, 274, 275, 305, 313, 399, 439
72, 74, 98, 99, 162:164, 167, 187, 190, 240, 244, 272, 274, 275, 302, 304, 305, 313, 399, 439
A2 (DAPAT_ARATH):129, 132, 344129, 132, 344

Full PDB list

2z1z, 2z20, 3ei5, 3ei6, 3ei7, 3ei8, 3ei9, 3eia, 3eib (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
Y
7
2
F
7
4
I
9
8
G
9
9
G
1
6
2
A
1
6
3
K
1
6
4
Y
1
8
7
Y
1
9
0
C
2
4
0
N
2
4
4
D
2
7
2
A
2
7
4
Y
2
7
5
S
3
0
2
S
3
0
4
K
3
0
5
R
3
1
3
Y
3
9
9
R
4
3
9
Y
1
2
9
N
3
4
4
[1]2z1z.a mlt,plp24 . . . . . . . . . . . . . . . . . . . . . .
[1]2z20.b plp15 . . . . . . . . . . . . . . . . . . . . . .
[1]3ei5.a pgu25 . . . . . . . . . . . . . . . . . . . . . .
[1]3ei6.a pl428 . . . . . . . . . . . . . . . . . . . . . .
[1]3ei7.a none . . . . . . . . . . . . . . . . . . . . . .
[1]3ei8.a plp15 . . . . . . . . . . . . . . . . N . . . . .
[1]3ei8.b pl528 . . . . . . . . . . . . . . . . N . . . . .
[1]3ei9.b pl625 . . . . . . . . . . . . . . . . N . . . . .
[1]3eia.b pl625 . . . . . . . . . . . . . . . . Q . . . . .

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
Y
7
2
F
7
4
I
9
8
G
9
9
G
1
6
2
A
1
6
3
K
1
6
4
I
1
6
7
Y
1
8
7
Y
1
9
0
C
2
4
0
N
2
4
4
D
2
7
2
A
2
7
4
Y
2
7
5
S
3
0
2
S
3
0
4
K
3
0
5
R
3
1
3
Y
3
9
9
R
4
3
9
Y
1
2
9
E
1
3
2
N
3
4
4
[1]2z1z.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]2z20.b . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ei5.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ei6.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]3ei7.a . . . . . . . . * . . . . . . . . * . . . . . .
[1]3ei8.a . . . . . . . . . . . . . . . . . N . . . . . .
[1]3ei8.b . . . . . . . . . . . . . . . . . N . . . . . .
[1]3ei9.b . . . . . . . . . . . . . . . . . N . . . . . .
[1]3eia.b . . . . . . . . . . . . . . . . . Q . . . . . .

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
2z1z.a:mlt,plp
2z20.b:plp
3ei5.a:pgu
3ei6.a:pl4
3ei7.a is apo
3ei8.a:plp
3ei8.b:pl5
3ei9.b:pl6
3eia.b:pl6
[1] 2z1z.a
0.3
0 0.4 0.9 - 0.3 0.6 0.4 0.3
[1] 2z20.b 0.5
0
0.5 1.0 - 0 0.8 0.4 0.4
[1] 3ei5.a 0.6 0.1
0.2
1.0 - 0.3 0.5 0.2 0.1
[1] 3ei6.a 0.4 0.1 0.3
0.3
- 0.2 0.3 0.4 0.3
[1] 3ei7.a 1.6 0.1 1.4 1.0
-
0.3 1.1 1.4 1.4
[1] 3ei8.a 0.2 0.1 0.2 0.3 -
0.1
0.4 0.2 0.1
[1] 3ei8.b 0.5 0.1 0.1 0.1 - 0.1
0.2
0 0.1
[1] 3ei9.b 0.4 0.1 0.1 0.8 - 0.1 0.6
0
0
[1] 3eia.b 0.5 0.3 0.3 0.9 - 0.2 0.5 0.2
0.2
[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
2z1z.a
2z20.b
3ei5.a
3ei6.a
3ei7.a
3ei8.a
3ei8.b
3ei9.b
3eia.b
[1] 2z1z.a
0
.04 .04 .05 .10 .03 .05 .04 .03
[1] 2z20.b .04
0
.05 .08 .09 .06 .08 .05 .05
[1] 3ei5.a .04 .05
0
.05 .10 .04 .04 .03 .02
[1] 3ei6.a .05 .08 .05
0
.11 .03 .01 .04 .05
[1] 3ei7.a .10 .09 .10 .11
0
.11 .11 .11 .11
[1] 3ei8.a .03 .06 .04 .03 .11
0
.03 .04 .04
[1] 3ei8.b .05 .08 .04 .01 .11 .03
0
.03 .03
[1] 3ei9.b .04 .05 .03 .04 .11 .04 .03
0
0
[1] 3eia.b .03 .05 .02 .05 .11 .04 .03 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
2z1z.a
2z20.b
3ei5.a
3ei6.a
3ei7.a
3ei8.a
3ei8.b
3ei9.b
3eia.b
[1] 2z1z.a
0
0.3 0.3 0.3 1.1 0.3 0.3 0.3 0.3
[1] 2z20.b 0.3
0
0.3 0.4 1.2 0.2 0.3 0.2 0.2
[1] 3ei5.a 0.3 0.3
0
0.2 1.1 0.3 0.3 0.3 0.2
[1] 3ei6.a 0.3 0.4 0.2
0
1.2 0.2 0.2 0.3 0.3
[1] 3ei7.a 1.1 1.2 1.1 1.2
0
1.2 1.3 1.2 1.2
[1] 3ei8.a 0.3 0.2 0.3 0.2 1.2
0
0.2 0.2 0.2
[1] 3ei8.b 0.3 0.3 0.3 0.2 1.3 0.2
0
0.1 0.2
[1] 3ei9.b 0.3 0.2 0.3 0.3 1.2 0.2 0.1
0
0.2
[1] 3eia.b 0.3 0.2 0.2 0.3 1.2 0.2 0.2 0.2
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
2z1z.a
2z20.b
3ei5.a
3ei6.a
3ei7.a
3ei8.a
3ei8.b
3ei9.b
3eia.b
[1] 2z1z.a
0
0.5 0.8 0.9 1.6 0.6 0.6 0.5 0.8
[1] 2z20.b 0.5
0
0.8 0.9 1.6 0.5 0.6 0.4 0.8
[1] 3ei5.a 0.8 0.8
0
0.5 1.8 0.8 0.8 0.7 0.3
[1] 3ei6.a 0.9 0.9 0.5
0
1.8 0.8 0.7 0.8 0.5
[1] 3ei7.a 1.6 1.6 1.8 1.8
0
1.6 1.7 1.7 1.8
[1] 3ei8.a 0.6 0.5 0.8 0.8 1.6
0
0.4 0.4 0.8
[1] 3ei8.b 0.6 0.6 0.8 0.7 1.7 0.4
0
0.4 0.8
[1] 3ei9.b 0.5 0.4 0.7 0.8 1.7 0.4 0.4
0
0.7
[1] 3eia.b 0.8 0.8 0.3 0.5 1.8 0.8 0.8 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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