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DHAS1_VIBCH_1_370

Aspartate-semialdehyde dehydrogenase 1 [Aspartate-semialdehyde dehydrogenase family]

Composition of the binding site

Protein chains monomer
A1 (DHAS1_VIBCH):7, 9:12, 35:37, 71:74, 96:98, 101, 133, 134, 161, 164:166, 229, 240, 243, 267, 274, 350, 351, 354, 3557, 9:12, 35:37, 71:74, 96:98, 101, 133, 134, 161, 164:166, 229, 240, 243, 267, 274, 350, 351, 354, 355

Full PDB list

1mb4, 1mc4, 3pzr, 3q0e, 4r5m

Pocket contact map

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PDB.ch
   
ligand
A1
G
7
R
9
G
1
0
M
1
1
V
1
2
S
3
5
T
3
6
S
3
7
C
7
1
Q
7
2
G
7
3
G
7
4
A
9
6
A
9
7
S
9
8
R
1
0
1
N
1
3
3
C
1
3
4
Q
1
6
1
S
1
6
4
G
1
6
5
I
2
2
9
E
2
4
0
K
2
4
3
R
2
6
7
H
2
7
4
Q
3
5
0
L
3
5
1
G
3
5
4
A
3
5
5
[1]1mb4.b C,ndp55 . . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]1mc4.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3pzr.a C,nap55 . . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]3q0e.a C7 . . . . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]4r5m.a 4no,nap64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
G
7
R
9
G
1
0
M
1
1
V
1
2
S
3
5
T
3
6
S
3
7
C
7
1
Q
7
2
G
7
3
G
7
4
A
9
6
A
9
7
S
9
8
R
1
0
1
N
1
3
3
C
1
3
4
Q
1
6
1
S
1
6
4
G
1
6
5
A
1
6
6
I
2
2
9
E
2
4
0
K
2
4
3
R
2
6
7
H
2
7
4
Q
3
5
0
L
3
5
1
G
3
5
4
A
3
5
5
[1]1mb4.b . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . .
[1]1mc4.a . . . . . . . . . . . . . . . . . * . . . . . . . . . * . . .
[1]3pzr.a . . . . . . . . . . . . . . . . . * . . . . . . . . . * . . .
[1]3q0e.a . . . . . . . . . . . . . . . . . * . . . . . . . . . * . . .
[1]4r5m.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
1mb4.b:C,ndp
1mc4.a is apo
3pzr.a:C,nap
3q0e.a:C
4r5m.a:4no,nap
[1] 1mb4.b
0.4
- 0.8 0.6 0.5
[1] 1mc4.a 1.8
-
1.0 1.0 0.5
[1] 3pzr.a 1.9 -
0.4
0.8 0.2
[1] 3q0e.a 2.5 - 0.6
0.5
0.2
[1] 4r5m.a 2.2 - 1.0 0.8
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
1mb4.b
1mc4.a
3pzr.a
3q0e.a
4r5m.a
[1] 1mb4.b
0
.07 .07 .10 .07
[1] 1mc4.a .07
0
.07 .07 .07
[1] 3pzr.a .07 .07
0
.04 .02
[1] 3q0e.a .10 .07 .04
0
.04
[1] 4r5m.a .07 .07 .02 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1mb4.b
1mc4.a
3pzr.a
3q0e.a
4r5m.a
[1] 1mb4.b
0
0.4 0.4 0.4 0.4
[1] 1mc4.a 0.4
0
0.5 0.4 0.5
[1] 3pzr.a 0.4 0.5
0
0.5 0.6
[1] 3q0e.a 0.4 0.4 0.5
0
0.2
[1] 4r5m.a 0.4 0.5 0.6 0.2
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
1mb4.b
1mc4.a
3pzr.a
3q0e.a
4r5m.a
[1] 1mb4.b
0
0.8 0.6 0.8 0.6
[1] 1mc4.a 0.8
0
0.8 0.7 0.8
[1] 3pzr.a 0.6 0.8
0
0.8 0.6
[1] 3q0e.a 0.8 0.7 0.8
0
0.6
[1] 4r5m.a 0.6 0.8 0.6 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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