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ARGD_SALTY_1_405

Acetylornithine/succinyldiaminopimelate aminotransferase [Class-III pyridoxal-phosphate-dependent aminotransferase family. ArgD subfamily]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (ARGD_SALTY):R: Pyridoxal phosphate binding (108, 109)
R: Pyridoxal phosphate binding (226, 228, 229)
51, 107, 112, 141:144, 193, 198, 255, 377
51, 107:109, 112, 141:144, 193, 198, 226, 228, 229, 255, 377
A2 (ARGD_SALTY):79, 282:28479, 282:284

Full PDB list

2pb0, 2pb2, 4jev, 4jew, 4jex, 4jey, 4jez, 4jf0, 4jf1 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
I
5
1
S
1
0
7
G
1
0
8
T
1
0
9
N
1
1
2
F
1
4
1
H
1
4
2
G
1
4
3
R
1
4
4
E
1
9
3
E
1
9
8
D
2
2
6
V
2
2
8
Q
2
2
9
K
2
5
5
R
3
7
7
G
2
8
2
S
2
8
3
T
2
8
4
[1]2pb0.a plp15 . . . . . . . . . . . . . . * . . . .
[1]2pb2.b none . . . . . . . . . . . . . . . . . . .
[1]4jev.a pxg25 . . . . . . . . . . . . . . . . . . .
[1]4jew.a p0024 . . . . . . . . . . . . . . . . . . .
[1]4jey.a plp16 . . . . . . . . . . A . . . . . . . .
[1]4jez.a p0019 . . . . . . . . . . . . . . . . . . .
[1]4jf1.a plp15 . . . . . . . . Q . . . . . . . . . .
[2]4jf0.b 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 A2
I
5
1
S
1
0
7
G
1
0
8
T
1
0
9
N
1
1
2
F
1
4
1
H
1
4
2
G
1
4
3
R
1
4
4
E
1
9
3
E
1
9
8
D
2
2
6
V
2
2
8
Q
2
2
9
K
2
5
5
R
3
7
7
N
7
9
G
2
8
2
S
2
8
3
T
2
8
4
[1]2pb0.a . . . . . . . . * . * . . . * . . . . .
[1]2pb2.b . . . . . . . . . . * . . . . . . . . .
[1]4jev.a . . . . . . . . . . . . . . . . . . . .
[1]4jew.a . . . . . . . . . . * . . . . . . . . .
[1]4jey.a . . . . . . . . . . A . . . . . . . . .
[1]4jez.a . . . . . . . . . . * . . . . . R . . .
[1]4jf1.a . . . . . . . . Q . * . . . . . . . . .
[2]4jf0.b . . . . . . . . . . * . . . it1 . R . . .

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
2pb0.a:plp
2pb2.b is apo
4jev.a:pxg
4jew.a:p00
4jey.a:plp
4jez.a:p00
4jf1.a:plp
4jf0.b is apo
[1] 2pb0.a
0.9
- 2.2 2.9 0.4 0.6 0.5 -
[1] 2pb2.b 0.2
-
1.5 0.4 0.2 0.1 0.2 -
[1] 4jev.a 0.1 -
0.4
0 0 0.3 0 -
[1] 4jew.a 0.1 - 2.0
0
0 0.2 0 -
[1] 4jey.a 0.1 - 0.3 0.3
0
0.1 0 -
[1] 4jez.a 0.2 - 2.1 0.2 0.2
0
0 -
[1] 4jf1.a 0.1 - 1.9 0.3 0.2 0.1
0
-
[2] 4jf0.b 11 - 13 11 11 12 11
-
[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
2pb0.a
2pb2.b
4jev.a
4jew.a
4jey.a
4jez.a
4jf1.a
4jf0.b
[1] 2pb0.a
0
.17 .22 .20 .23 .20 .18 .70
[1] 2pb2.b .17
0
.08 .06 .07 .04 .03 .62
[1] 4jev.a .22 .08
0
.08 .05 .10 .09 .68
[1] 4jew.a .20 .06 .08
0
.11 .02 .03 .61
[1] 4jey.a .23 .07 .05 .11
0
.11 .09 .69
[1] 4jez.a .20 .04 .10 .02 .11
0
.02 .59
[1] 4jf1.a .18 .03 .09 .03 .09 .02
0
.60
[2] 4jf0.b .70 .62 .68 .61 .69 .59 .60
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2pb0.a
2pb2.b
4jev.a
4jew.a
4jey.a
4jez.a
4jf1.a
4jf0.b
[1] 2pb0.a
0
6.0 0.3 0.4 0.3 5.8 0.3 5.8
[1] 2pb2.b 6.0
0
6.0 6.0 6.0 0.2 6.0 0.3
[1] 4jev.a 0.3 6.0
0
0.1 0.1 5.8 0.1 5.8
[1] 4jew.a 0.4 6.0 0.1
0
0.1 5.8 0.2 5.8
[1] 4jey.a 0.3 6.0 0.1 0.1
0
5.8 0.1 5.8
[1] 4jez.a 5.8 0.2 5.8 5.8 5.8
0
5.8 0.3
[1] 4jf1.a 0.3 6.0 0.1 0.2 0.1 5.8
0
5.8
[2] 4jf0.b 5.8 0.3 5.8 5.8 5.8 0.3 5.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
2pb0.a
2pb2.b
4jev.a
4jew.a
4jey.a
4jez.a
4jf1.a
4jf0.b
[1] 2pb0.a
0
5.3 0.8 0.8 0.7 5.3 0.5 5.2
[1] 2pb2.b 5.3
0
5.3 5.3 5.4 0.6 5.4 0.6
[1] 4jev.a 0.8 5.3
0
0.4 0.2 5.3 0.5 5.2
[1] 4jew.a 0.8 5.3 0.4
0
0.2 5.3 0.3 5.2
[1] 4jey.a 0.7 5.4 0.2 0.2
0
5.4 0.3 5.3
[1] 4jez.a 5.3 0.6 5.3 5.3 5.4
0
5.3 0.4
[1] 4jf1.a 0.5 5.4 0.5 0.3 0.3 5.3
0
5.3
[2] 4jf0.b 5.2 0.6 5.2 5.2 5.3 0.4 5.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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