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DHOM_YEAST_2_359

Homoserine dehydrogenase [Homoserine dehydrogenase family]

Composition of the binding site

Protein chains monomer
A1 (DHOM_YEAST):11:17, 39:41, 73, 92:95, 97, 98, 115:117, 144, 174:176, 206, 208, 214, 219, 223, 338:340, 34411:17, 39:41, 73, 92:95, 97, 98, 115:117, 144, 174:176, 206, 208, 214, 219, 223, 338:340, 344
Metals (Me):Na

Full PDB list

1ebf, 1ebu, 1q7g, 1tve

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
1
1
G
1
2
A
1
3
G
1
4
V
1
5
V
1
6
G
1
7
E
4
0
A
4
1
N
9
2
T
9
3
S
9
4
I
9
8
P
1
1
5
N
1
1
6
K
1
1
7
A
1
4
4
S
1
7
4
G
1
7
5
T
1
7
6
Y
2
0
6
E
2
0
8
D
2
1
4
D
2
1
9
K
2
2
3
G
3
3
8
A
3
3
9
G
3
4
0
T
3
4
4
[1]1ebf.a nad44 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]1ebu.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]1ebu.d hse,nda51 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]1q7g.a nho54 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]1tve.b 17811 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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 Me
I
1
1
G
1
2
A
1
3
G
1
4
V
1
5
V
1
6
G
1
7
A
3
9
E
4
0
A
4
1
L
7
3
N
9
2
T
9
3
S
9
4
S
9
5
Y
9
7
I
9
8
P
1
1
5
N
1
1
6
K
1
1
7
A
1
4
4
S
1
7
4
G
1
7
5
T
1
7
6
Y
2
0
6
E
2
0
8
D
2
1
4
D
2
1
9
K
2
2
3
G
3
3
8
A
3
3
9
G
3
4
0
T
3
4
4
[1]1ebf.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]1ebu.b . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]1ebu.d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]1q7g.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]1tve.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
1ebf.a:nad
1ebu.b is apo
1ebu.d:hse,nda
1q7g.a:nho
1tve.b:178
[1] 1ebf.a
0
- 0.2 0.3 0.1
[1] 1ebu.b 1.7
-
1.3 1.7 0.1
[1] 1ebu.d 0.5 -
0
1.5 0.1
[1] 1q7g.a 0.1 - 0.2
0.1
0
[1] 1tve.b 1.3 - 0.9 1.7
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
1ebf.a
1ebu.b
1ebu.d
1q7g.a
1tve.b
[1] 1ebf.a
0
.07 .05 .02 .06
[1] 1ebu.b .07
0
.07 .07 .04
[1] 1ebu.d .05 .07
0
.06 .06
[1] 1q7g.a .02 .07 .06
0
.06
[1] 1tve.b .06 .04 .06 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1ebf.a
1ebu.b
1ebu.d
1q7g.a
1tve.b
[1] 1ebf.a
0
0.8 0.8 0.5 1.0
[1] 1ebu.b 0.8
0
0.5 1.0 0.7
[1] 1ebu.d 0.8 0.5
0
1.0 0.8
[1] 1q7g.a 0.5 1.0 1.0
0
1.1
[1] 1tve.b 1.0 0.7 0.8 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
1ebf.a
1ebu.b
1ebu.d
1q7g.a
1tve.b
[1] 1ebf.a
0
1.1 1.0 0.8 1.4
[1] 1ebu.b 1.1
0
0.7 1.2 0.9
[1] 1ebu.d 1.0 0.7
0
1.3 1.1
[1] 1q7g.a 0.8 1.2 1.3
0
1.4
[1] 1tve.b 1.4 0.9 1.1 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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