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COAA_ECOLI_2_316

Pantothenate kinase [Prokaryotic pantothenate kinase family]

Composition of the binding site

Protein chains monomer
A1 (COAA_ECOLI):41:46, 55, 96:103, 106, 127, 130, 143, 145, 146, 151, 175, 177, 178, 180, 199, 201, 240, 243, 244, 247:252, 258, 259, 262, 277, 281, 282, 303, 306, 30741:46, 55, 96:103, 106, 127, 130, 143, 145, 146, 151, 175, 177, 178, 180, 199, 201, 240, 243, 244, 247:252, 258, 259, 262, 277, 281, 282, 303, 306, 307

Full PDB list

1esm, 1esn, 1sq5, 4f7w, 4gi7, 4ne2

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
4
1
I
4
2
N
4
3
D
4
5
L
4
6
Y
5
5
V
9
7
A
9
8
V
9
9
G
1
0
0
K
1
0
1
S
1
0
2
T
1
0
3
R
1
0
6
D
1
2
7
L
1
3
0
K
1
4
5
G
1
4
6
Y
1
7
5
H
1
7
7
Y
1
8
0
E
1
9
9
L
2
0
1
Y
2
4
0
R
2
4
3
F
2
4
4
F
2
4
7
F
2
5
2
Y
2
5
8
F
2
5
9
Y
2
6
2
L
2
7
7
I
2
8
1
N
2
8
2
K
3
0
3
H
3
0
7
[1]1sq5.d adp,pau42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4f7w.a adp,pn447 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4gi7.d 0jr,adp49 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ne2.a adp,mg,sh254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]1esn.a anp,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[3]1esm.a 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

[download in TSV format]
   
PDB.ch
A1
G
4
1
I
4
2
N
4
3
E
4
4
D
4
5
L
4
6
Y
5
5
S
9
6
V
9
7
A
9
8
V
9
9
G
1
0
0
K
1
0
1
S
1
0
2
T
1
0
3
R
1
0
6
D
1
2
7
L
1
3
0
K
1
4
3
K
1
4
5
G
1
4
6
Y
1
5
1
Y
1
7
5
H
1
7
7
L
1
7
8
Y
1
8
0
E
1
9
9
L
2
0
1
Y
2
4
0
R
2
4
3
F
2
4
4
F
2
4
7
R
2
4
8
E
2
4
9
G
2
5
0
A
2
5
1
F
2
5
2
Y
2
5
8
F
2
5
9
Y
2
6
2
L
2
7
7
I
2
8
1
N
2
8
2
K
3
0
3
N
3
0
6
H
3
0
7
[1]1sq5.d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . * . . . . . . . .
[1]4f7w.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]4gi7.d . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]4ne2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . * . . . . . . . .
[2]1esn.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . * . * . . . . . . . . . . . .
[3]1esm.a * * . * * . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . .

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
1sq5.d:adp,pau
4f7w.a:adp,pn4
4gi7.d:0jr,adp
4ne2.a:adp,mg,sh2
1esn.a:anp,mg
1esm.a:coa
[1] 1sq5.d
0.1
1.4 1.8 0.7 1.8 1.8
[1] 4f7w.a 0.2
0.1
0.4 0.7 2.2 2.8
[1] 4gi7.d 0.3 0.1
0
0.6 2.0 2.2
[1] 4ne2.a 0.4 1.9 1.5
0.3
2.1 2.8
[2] 1esn.a 3.0 8.7 7.8 7.1
0.1
5.5
[3] 1esm.a 8.1 10 10 8.2 10
0.2
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
1sq5.d
4f7w.a
4gi7.d
4ne2.a
1esn.a
1esm.a
[1] 1sq5.d
0
.07 .07 .05 .33 .35
[1] 4f7w.a .07
0
.04 .09 .31 .33
[1] 4gi7.d .07 .04
0
.10 .31 .33
[1] 4ne2.a .05 .09 .10
0
.32 .34
[2] 1esn.a .33 .31 .31 .32
0
.54
[3] 1esm.a .35 .33 .33 .34 .54
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.2 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
1sq5.d
4f7w.a
4gi7.d
4ne2.a
1esn.a
1esm.a
[1] 1sq5.d
0
0.5 0.6 0.5 3.5 2.8
[1] 4f7w.a 0.5
0
0.4 0.7 3.7 2.8
[1] 4gi7.d 0.6 0.4
0
0.8 3.7 2.9
[1] 4ne2.a 0.5 0.7 0.8
0
3.3 2.7
[2] 1esn.a 3.5 3.7 3.7 3.3
0
4.2
[3] 1esm.a 2.8 2.8 2.9 2.7 4.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.8 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
1sq5.d
4f7w.a
4gi7.d
4ne2.a
1esn.a
1esm.a
[1] 1sq5.d
0
1.0 1.1 1.1 3.8 3.4
[1] 4f7w.a 1.0
0
0.7 1.0 4.0 3.4
[1] 4gi7.d 1.1 0.7
0
1.0 4.0 3.4
[1] 4ne2.a 1.1 1.0 1.0
0
3.7 3.3
[2] 1esn.a 3.8 4.0 4.0 3.7
0
4.5
[3] 1esm.a 3.4 3.4 3.4 3.3 4.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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