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COAD_ENTFA_1_163

Phosphopantetheine adenylyltransferase [Bacterial CoaD family]

Composition of the binding site

Protein chains homodimer
A1 (COAD_ENTFA):8:10, 37, 72:75, 89, 99, 103, 106, 1078:10, 37, 72:75, 89, 99, 103, 106, 107
A2 (COAD_ENTFA):132, 135, 136, 139132, 135, 136, 139

Full PDB list

3nd5, 3nd6, 3nd7 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 A2
P
8
T
7
2
Q
7
3
L
7
4
T
7
5
R
8
9
Y
9
9
I
1
0
3
M
1
0
6
N
1
0
7
L
1
3
2
E
1
3
5
V
1
3
6
F
1
3
9
[1]3nd6.d none . . . . . . . . . . . . . .
[1]3nd7.c pny18 . . . . . . . . . . . . . .

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 A2
P
8
G
9
S
1
0
F
3
7
T
7
2
Q
7
3
L
7
4
T
7
5
R
8
9
Y
9
9
I
1
0
3
M
1
0
6
N
1
0
7
L
1
3
2
E
1
3
5
V
1
3
6
F
1
3
9
[1]3nd6.d . . . . . . . . . . . . . . . . .
[1]3nd7.c . . . . . . . . . . . . . . . . .

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
3nd6.d is apo
3nd7.c:pny
[1] 3nd6.d
-
0
[1] 3nd7.c -
0
[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
3nd6.d
3nd7.c
[1] 3nd6.d
0
0
[1] 3nd7.c 0
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
3nd6.d
3nd7.c
[1] 3nd6.d
0
0.5
[1] 3nd7.c 0.5
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
3nd6.d
3nd7.c
[1] 3nd6.d
0
0.7
[1] 3nd7.c 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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