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DDAH_PSEAE_1_254

N(G),N(G)-dimethylarginine dimethylaminohydrolase [DDAH family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DDAH_PSEAE):R: Substrate binding (65, 66)
18, 60, 63, 85, 116, 132, 161, 162, 165, 243:246, 249
18, 60, 63, 65, 66, 85, 116, 132, 161, 162, 165, 243:246, 249

Full PDB list

1h70, 3bpb, 3rhy

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
8
D
6
0
F
6
3
E
6
5
D
6
6
R
8
5
G
1
1
6
R
1
3
2
H
1
6
2
I
2
4
3
D
2
4
4
C
2
4
9
[1]1h70.a cir12 . . . . . . . . . . . S
[1]3bpb.a smz11 . . . . . . . . G . . *
[1]3rhy.a hm38 - . . . . . . . . . . *

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
L
1
8
D
6
0
F
6
3
E
6
5
D
6
6
R
8
5
G
1
1
6
R
1
3
2
L
1
6
1
H
1
6
2
T
1
6
5
I
2
4
3
D
2
4
4
G
2
4
5
G
2
4
6
C
2
4
9
[1]1h70.a . . . . . . . . * . . . . . . S
[1]3bpb.a . . . . . . . . . G . . . . . *
[1]3rhy.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
1h70.a:cir
3bpb.a:smz
3rhy.a:hm3
[1] 1h70.a
0
0.1 1.4
[1] 3bpb.a 0.6
0.5
0.7
[1] 3rhy.a 0.3 0.4
0.4
[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
1h70.a
3bpb.a
3rhy.a
[1] 1h70.a
0
.11 .09
[1] 3bpb.a .11
0
.03
[1] 3rhy.a .09 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1h70.a
3bpb.a
3rhy.a
[1] 1h70.a
0
0.6 0.5
[1] 3bpb.a 0.6
0
0.5
[1] 3rhy.a 0.5 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1h70.a
3bpb.a
3rhy.a
[1] 1h70.a
0
0.9 0.5
[1] 3bpb.a 0.9
0
0.5
[1] 3rhy.a 0.5 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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