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ARD1_YEAST_1_238

N-terminal acetyltransferase A complex catalytic subunit ARD1 [Acetyltransferase family. ARD1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ARD1_YEAST):D: N-acetyltransferase (50:54, 56:62, 78:82, 84, 85, 88, 91, 121, 123, 124)
20
20, 50:54, 56:62, 78:82, 84, 85, 88, 91, 121, 123, 124

Full PDB list

4hnw, 4hnx, 4hny, 4xnh, 4xpd (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
K
8
0
L
8
1
D
8
2
Y
8
5
P
8
8
K
9
1
T
1
2
3
Y
1
2
4
[1]4hnw.b ihp36 . . . . . . . .
[1]4hnx.b g4p36 . . . . . . . .
[1]4xnh.b i6p36 . . . . . . . .
[2]4hny.b none . - - - - . . .

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
N
2
0
T
5
0
T
5
1
L
5
2
D
5
3
C
5
4
D
5
6
S
5
7
D
5
8
E
5
9
Q
6
0
D
6
1
E
6
2
T
7
8
I
7
9
K
8
0
L
8
1
D
8
2
T
8
4
Y
8
5
P
8
8
K
9
1
M
1
2
1
T
1
2
3
Y
1
2
4
[1]4hnw.b . . . . . . . - - - - - - . . * . . . . . * . . .
[1]4hnx.b . . . . . . - - - - - - - - . . . . . . . . . . .
[1]4xnh.b . . . . . . . - - - - - - . . * . . . . . . . . .
[2]4hny.b . . . * * . . . * * * * . . . . - - - - - . . . .

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
4hnw.b:ihp
4hnx.b:g4p
4xnh.b:i6p
4hny.b is apo
[1] 4hnw.b
0.1
3.3 0.6 -
[1] 4hnx.b 0.1
0
0.4 -
[1] 4xnh.b 0.1 6.1
0.2
-
[2] 4hny.b 8.1 13 5.9
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
4hnw.b
4hnx.b
4xnh.b
4hny.b
[1] 4hnw.b
0
.14 .18 .72
[1] 4hnx.b .14
0
.25 .58
[1] 4xnh.b .18 .25
0
.82
[2] 4hny.b .72 .58 .82
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.6 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
4hnw.b
4hnx.b
4xnh.b
4hny.b
[1] 4hnw.b
0
2.6 0.8 14
[1] 4hnx.b 2.6
0
2.7 11
[1] 4xnh.b 0.8 2.7
0
14
[2] 4hny.b 14 11 14
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.6 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
4hnw.b
4hnx.b
4xnh.b
4hny.b
[1] 4hnw.b
0
2.5 1.1 14
[1] 4hnx.b 2.5
0
2.6 11
[1] 4xnh.b 1.1 2.6
0
14
[2] 4hny.b 14 11 14
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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