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AMD_RAT_44_355

Peptidyl-glycine alpha-amidating monooxygenase

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AMD_RAT):R: Peptidylglycine alpha-hydroxylating monooxygenase (55, 57:63, 88, 90:92, 96:98, 100, 110, 112, 134:137, 170, 190:192, 194, 195, 206, 208, 240, 242, 306, 314, 316, 318)55, 57:63, 88, 90:92, 96:98, 100, 110, 112, 134:137, 170, 190:192, 194, 195, 206, 208, 240, 242, 306, 314, 316, 318
Metals (Me):Cu

Full PDB list

1opm, 1phm, 1sdw, 1yi9, 1yip, 1yjk, 1yjl, 3mib, 3mic, 3mid, 3mie, 3mif, 3mig, 3mih, 3mlj, 3mlk, 3mll, 3phm, 4e4z (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
T
5
5
L
5
7
D
5
8
A
5
9
S
6
0
D
6
1
F
6
2
A
6
3
V
8
8
E
9
0
E
9
1
A
9
2
D
9
6
F
9
7
K
9
8
L
1
1
0
F
1
1
2
K
1
3
4
A
1
3
5
N
1
3
6
I
1
3
7
Q
1
7
0
S
1
9
0
V
1
9
1
H
1
9
2
R
1
9
5
L
2
0
6
M
2
0
8
R
2
4
0
H
2
4
2
I
3
0
6
M
3
1
4
N
3
1
6
Y
3
1
8
[1]1opm.a iyg22 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cu
[1]1phm.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cu
[1]1sdw.a iyt.iyt.iyt75 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cu
[1]1yi9.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - I . . Cu

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
T
5
5
L
5
7
D
5
8
A
5
9
S
6
0
D
6
1
F
6
2
A
6
3
V
8
8
E
9
0
E
9
1
A
9
2
D
9
6
F
9
7
K
9
8
R
1
0
0
L
1
1
0
F
1
1
2
K
1
3
4
A
1
3
5
N
1
3
6
I
1
3
7
Q
1
7
0
S
1
9
0
V
1
9
1
H
1
9
2
T
1
9
4
R
1
9
5
L
2
0
6
M
2
0
8
R
2
4
0
H
2
4
2
I
3
0
6
M
3
1
4
N
3
1
6
Y
3
1
8
[1]1opm.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . Cu
[1]1phm.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . Cu
[1]1sdw.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cu
[1]1yi9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . - I . . Cu

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
1opm.a:iyg
1phm.a is apo
1sdw.a:iyt.iyt.iyt
1yi9.a is apo
[1] 1opm.a
0.1
- 2.9 -
[1] 1phm.a 0.8
-
3.7 -
[1] 1sdw.a 0.2 -
0.5
-
[1] 1yi9.a 1.3 - 4.6
-
[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
1opm.a
1phm.a
1sdw.a
1yi9.a
[1] 1opm.a
0
.03 .07 .06
[1] 1phm.a .03
0
.10 .05
[1] 1sdw.a .07 .10
0
.12
[1] 1yi9.a .06 .05 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1opm.a
1phm.a
1sdw.a
1yi9.a
[1] 1opm.a
0
0.2 0.3 0.8
[1] 1phm.a 0.2
0
0.3 0.8
[1] 1sdw.a 0.3 0.3
0
0.9
[1] 1yi9.a 0.8 0.8 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1opm.a
1phm.a
1sdw.a
1yi9.a
[1] 1opm.a
0
0.4 0.7 1.4
[1] 1phm.a 0.4
0
0.8 1.4
[1] 1sdw.a 0.7 0.8
0
1.5
[1] 1yi9.a 1.4 1.4 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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