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ARG56_YEAST_58_356

Protein ARG5,6, mitochondrial

Composition of the binding site

Protein chains monomer
A1 (ARG56_YEAST):135:137, 157, 158, 168, 172, 211, 247:250135:137, 157, 158, 168, 172, 211, 247:250

Full PDB list

3zzf, 3zzg, 3zzh, 4ab7 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
1
3
5
T
1
3
6
G
1
3
7
R
1
5
8
V
1
6
8
F
1
7
2
N
2
4
7
V
2
4
8
N
2
4
9
A
2
5
0
[1]3zzg.a none . . . . . . . . . .
[1]4ab7.d nlg13 . . . . . . . . . .

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
1
3
5
T
1
3
6
G
1
3
7
I
1
5
7
R
1
5
8
V
1
6
8
F
1
7
2
V
2
1
1
N
2
4
7
V
2
4
8
N
2
4
9
A
2
5
0
[1]3zzg.a . . . . . . . . . . . .
[1]4ab7.d . . . . . . . . . . . .

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
3zzg.a is apo
4ab7.d:nlg
[1] 3zzg.a
-
0.7
[1] 4ab7.d -
0.3
[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
3zzg.a
4ab7.d
[1] 3zzg.a
0
.05
[1] 4ab7.d .05
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
3zzg.a
4ab7.d
[1] 3zzg.a
0
0.8
[1] 4ab7.d 0.8
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

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
3zzg.a
4ab7.d
[1] 3zzg.a
0
0.9
[1] 4ab7.d 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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