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DHPH_RHOSO_2_356

Phenylalanine dehydrogenase [Glu/Leu/Phe/Val dehydrogenases family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DHPH_RHOSO):R: Substrate binding (118, 119)
39:41, 64, 67, 68, 79, 116, 117, 138, 263, 292, 293, 296, 297
39:41, 64, 67, 68, 79, 116:119, 138, 263, 292, 293, 296, 297
Cofactors (cF):nad/nai
Metals (Me):K

Full PDB list

1bw9, 1bxg, 1c1d, 1c1x

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
A
3
9
G
4
0
G
4
1
M
6
4
K
6
7
M
6
8
K
7
9
T
1
1
6
G
1
1
7
P
1
1
8
D
1
1
9
F
1
3
8
N
2
6
3
G
2
9
2
A
2
9
3
L
2
9
6
V
2
9
7
[1]1bw9.a ppy12 . . . . . . . . . . . . . . . . . nad K
[1]1bxg.b hci11 . . . . . . . . . . . . . . . . . nad
[1]1c1d.a F12 . . . . . . . . . . . . . . . . . nai K
[1]1c1x.a hfa12 . . . . . . . . . . . . . . . . . nad K

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 cF Me
A
3
9
G
4
0
G
4
1
M
6
4
K
6
7
M
6
8
K
7
9
T
1
1
6
G
1
1
7
P
1
1
8
D
1
1
9
F
1
3
8
N
2
6
3
G
2
9
2
A
2
9
3
L
2
9
6
V
2
9
7
[1]1bw9.a . . . . . . . . . . . . . . . . . nad K
[1]1bxg.b . . . . . . . . . . . . . . . . . nad
[1]1c1d.a . . . . . . . . . . . . . . . . . nai K
[1]1c1x.a . . . . . . . . . . . . . . . . . nad K

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
1bw9.a:ppy
1bxg.b:hci
1c1d.a:F
1c1x.a:hfa
[1] 1bw9.a
0.1
0.3 0.1 0.2
[1] 1bxg.b 0.1
0.1
0 0.3
[1] 1c1d.a 0 0.1
0
0
[1] 1c1x.a 0 0.3 0.1
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
1bw9.a
1bxg.b
1c1d.a
1c1x.a
[1] 1bw9.a
0
.04 .02 .01
[1] 1bxg.b .04
0
.03 .04
[1] 1c1d.a .02 .03
0
.01
[1] 1c1x.a .01 .04 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1bw9.a
1bxg.b
1c1d.a
1c1x.a
[1] 1bw9.a
0
0.3 0.2 0.2
[1] 1bxg.b 0.3
0
0.2 0.3
[1] 1c1d.a 0.2 0.2
0
0.2
[1] 1c1x.a 0.2 0.3 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1bw9.a
1bxg.b
1c1d.a
1c1x.a
[1] 1bw9.a
0
0.6 0.5 0.4
[1] 1bxg.b 0.6
0
0.3 0.5
[1] 1c1d.a 0.5 0.3
0
0.3
[1] 1c1x.a 0.4 0.5 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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