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AMD_RAT_498_820

Peptidyl-glycine alpha-amidating monooxygenase

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMD_RAT):R: Peptidyl-alpha-hydroxyglycine alpha- amidating lyase (533, 538, 585, 654, 706, 784)533, 538, 585, 654, 706, 784
Metals (Me):Ca/Hg/Zn

Full PDB list

3fvz, 3fw0

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
R
5
3
3
W
5
3
8
Y
6
5
4
R
7
0
6
M
7
8
4
[1]3fvz.a none . . . . . Ca,Zn
[1]3fw0.a hh314 . . . . . Ca,Hg

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
R
5
3
3
W
5
3
8
H
5
8
5
Y
6
5
4
R
7
0
6
M
7
8
4
[1]3fvz.a . . . . . . Ca,Zn
[1]3fw0.a . . . . . . Ca,Hg

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
3fvz.a is apo
3fw0.a:hh3
[1] 3fvz.a
-
0.2
[1] 3fw0.a -
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
3fvz.a
3fw0.a
[1] 3fvz.a
0
0
[1] 3fw0.a 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
3fvz.a
3fw0.a
[1] 3fvz.a
0
0.2
[1] 3fw0.a 0.2
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
3fvz.a
3fw0.a
[1] 3fvz.a
0
0.3
[1] 3fw0.a 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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