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ATDA_VIBCH_1_173_catalytic

Spermidine N(1)-acetyltransferase [Acetyltransferase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ATDA_VIBCH):D: N-acetyltransferase (27, 30, 31, 85:89, 94:100, 121:123, 127, 129, 130, 132:134, 136)
R: Substrate binding (85, 86)
27, 30, 31, 85:89, 94:100, 121:123, 127, 129, 130, 132:134, 136

Full PDB list

4jjx, 4jly, 4mhd, 4mi4, 4mj8, 4ncz, 4r57, 4r87, 4ygo, 5cnp, 5ug4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
2
7
Y
3
0
W
3
1
Q
8
6
I
8
7
I
8
8
I
8
9
Q
9
4
G
9
5
K
9
6
G
9
7
F
9
8
A
9
9
R
1
0
0
H
1
2
2
V
1
2
3
N
1
2
7
K
1
2
9
A
1
3
0
H
1
3
2
L
1
3
3
Y
1
3
4
[1]4mj8.c none . . . . . . . . . . . . . . . . . . . . . .
[1]4r57.a aco51 . . . . . . . . . . . . . . . . . . . . . .
[1]4r87.e coa48 . . . . . . . . . . . . . . . . . . . . . .

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
I
2
7
Y
3
0
W
3
1
F
8
5
Q
8
6
I
8
7
I
8
8
I
8
9
Q
9
4
G
9
5
K
9
6
G
9
7
F
9
8
A
9
9
R
1
0
0
L
1
2
1
H
1
2
2
V
1
2
3
N
1
2
7
K
1
2
9
A
1
3
0
H
1
3
2
L
1
3
3
Y
1
3
4
E
1
3
6
[1]4mj8.c . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4r57.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4r87.e . . . . . . . . . . . . . . * . . . . . . . . . .

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
4mj8.c is apo
4r57.a:aco
4r87.e:coa
[1] 4mj8.c
-
1.6 1.7
[1] 4r57.a -
0.3
0.3
[1] 4r87.e - 1.3
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
4mj8.c
4r57.a
4r87.e
[1] 4mj8.c
0
.07 .07
[1] 4r57.a .07
0
.05
[1] 4r87.e .07 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
4mj8.c
4r57.a
4r87.e
[1] 4mj8.c
0
0.6 0.8
[1] 4r57.a 0.6
0
0.5
[1] 4r87.e 0.8 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

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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
4mj8.c
4r57.a
4r87.e
[1] 4mj8.c
0
1.1 1.2
[1] 4r57.a 1.1
0
0.9
[1] 4r87.e 1.2 0.9
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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