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ASTB_ECOLI_1_447

N-succinylarginine dihydrolase [Succinylarginine dihydrolase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ASTB_ECOLI):R: Substrate binding (137, 138)
17, 18, 107, 109, 110, 177, 212, 247, 248, 250, 359:361, 365
17:22, 25, 28, 107, 109, 110, 137, 138, 177, 212, 247, 248, 250, 359:361, 365

Full PDB list

1ynf, 1ynh, 1yni

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
1
7
A
1
9
G
2
0
L
2
1
S
2
2
N
2
5
S
2
8
W
1
0
7
A
1
0
9
N
1
1
0
H
1
3
7
R
1
3
8
A
1
7
7
R
2
1
2
F
2
4
7
H
2
4
8
D
2
5
0
N
3
5
9
G
3
6
0
G
3
6
1
C
3
6
5
[1]1ynf.a none . . - - - - - . . . . . . . . . . . . . .
[1]1ynh.a suo16 . . . . . . . . . . . . . . . . . . . . .
[1]1yni.a sug19 . . . . . . . . . . . . . . . . . . . . S

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
H
1
7
Y
1
8
A
1
9
G
2
0
L
2
1
S
2
2
N
2
5
S
2
8
W
1
0
7
A
1
0
9
N
1
1
0
H
1
3
7
R
1
3
8
A
1
7
7
R
2
1
2
F
2
4
7
H
2
4
8
D
2
5
0
N
3
5
9
G
3
6
0
G
3
6
1
C
3
6
5
[1]1ynf.a . . . - - - - - . . . . . . . . . . . . . .
[1]1ynh.a . . . . . . . . . . . . . . . . . . . . . .
[1]1yni.a . . . . . . . . . . . . . . . . . . . . . S

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
1ynf.a is apo
1ynh.a:suo
1yni.a:sug
[1] 1ynf.a
-
0.1 0.3
[1] 1ynh.a -
0.1
0.3
[1] 1yni.a - 0
0.1
[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
1ynf.a
1ynh.a
1yni.a
[1] 1ynf.a
0
0 .02
[1] 1ynh.a 0
0
.02
[1] 1yni.a .02 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1ynf.a
1ynh.a
1yni.a
[1] 1ynf.a
0
0.4 0.4
[1] 1ynh.a 0.4
0
0.1
[1] 1yni.a 0.4 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
1ynf.a
1ynh.a
1yni.a
[1] 1ynf.a
0
0.6 0.7
[1] 1ynh.a 0.6
0
0.3
[1] 1yni.a 0.7 0.3
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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