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COAW_STAA8_1_267

Type II pantothenate kinase [Type II pantothenate kinase family]

Composition of the binding site

Protein chains homodimer
A1 (COAW_STAA8):8:11, 13, 28, 70, 71, 98:102, 113, 116, 117, 121, 122, 125, 137, 224:226, 2288:11, 13, 28, 70, 71, 98:102, 113, 116, 117, 121, 122, 125, 137, 224:226, 228
A2 (COAW_STAA8):156, 159, 167, 170:173, 202, 206, 240156, 159, 167, 170:173, 202, 206, 240
Metals (Me):Mg

Full PDB list

2ews, 4m7x, 4m7y, 4nb4, 5elz, 5jic

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
G
8
G
9
T
1
0
L
1
1
K
1
3
L
2
8
E
7
0
F
7
1
G
9
8
T
9
9
G
1
0
0
T
1
0
1
S
1
0
2
R
1
1
3
G
1
1
6
I
1
1
7
G
1
2
1
G
1
2
2
Q
1
2
5
Y
1
3
7
G
2
2
4
S
2
2
5
S
2
2
6
H
2
2
8
V
1
5
6
I
1
5
9
I
1
6
7
D
1
7
0
L
1
7
1
T
1
7
2
A
1
7
3
E
2
0
2
T
2
0
6
Y
2
4
0
[1]2ews.a anp31 . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - - - - - Mg
[1]4m7x.a 27q,adp53 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4m7y.a 2gh,adp51 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4nb4.d adp,sh357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]5elz.a 3v9,adp56 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]5jic.a adp,n7e53 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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 A2 Me
G
8
G
9
T
1
0
L
1
1
K
1
3
L
2
8
E
7
0
F
7
1
G
9
8
T
9
9
G
1
0
0
T
1
0
1
S
1
0
2
R
1
1
3
G
1
1
6
I
1
1
7
G
1
2
1
G
1
2
2
Q
1
2
5
Y
1
3
7
G
2
2
4
S
2
2
5
S
2
2
6
H
2
2
8
V
1
5
6
I
1
5
9
I
1
6
7
D
1
7
0
L
1
7
1
T
1
7
2
A
1
7
3
E
2
0
2
T
2
0
6
Y
2
4
0
[1]2ews.a . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - - - - - Mg
[1]4m7x.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4m7y.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4nb4.d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]5elz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]5jic.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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
2ews.a:anp
4m7x.a:27q,adp
4m7y.a:2gh,adp
4nb4.d:adp,sh3
5elz.a:3v9,adp
5jic.a:adp,n7e
[1] 2ews.a
0
0.4 0.5 0.6 0.3 0.4
[1] 4m7x.a 0.2
0.1
0.1 0.2 0.1 0
[1] 4m7y.a 0.5 0
0
0.2 0 0
[1] 4nb4.d 0.4 0.1 0
0
0.1 0.1
[1] 5elz.a 0.3 0.2 0.1 0.1
0.1
0
[1] 5jic.a 0.2 0 0.1 0.3 0.1
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
2ews.a
4m7x.a
4m7y.a
4nb4.d
5elz.a
5jic.a
[1] 2ews.a
0
.03 .03 .03 .03 .03
[1] 4m7x.a .03
0
.02 .01 0 0
[1] 4m7y.a .03 .02
0
.01 .02 .02
[1] 4nb4.d .03 .01 .01
0
.01 .01
[1] 5elz.a .03 0 .02 .01
0
.01
[1] 5jic.a .03 0 .02 .01 .01
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
2ews.a
4m7x.a
4m7y.a
4nb4.d
5elz.a
5jic.a
[1] 2ews.a
0
0.5 0.6 0.6 0.5 0.5
[1] 4m7x.a 0.5
0
0.2 0.2 0.1 0.1
[1] 4m7y.a 0.6 0.2
0
0.3 0.2 0.2
[1] 4nb4.d 0.6 0.2 0.3
0
0.2 0.2
[1] 5elz.a 0.5 0.1 0.2 0.2
0
0.1
[1] 5jic.a 0.5 0.1 0.2 0.2 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2ews.a
4m7x.a
4m7y.a
4nb4.d
5elz.a
5jic.a
[1] 2ews.a
0
1.0 0.7 0.7 1.0 1.0
[1] 4m7x.a 1.0
0
0.7 0.7 0.2 0.2
[1] 4m7y.a 0.7 0.7
0
0.5 0.7 0.7
[1] 4nb4.d 0.7 0.7 0.5
0
0.7 0.7
[1] 5elz.a 1.0 0.2 0.7 0.7
0
0.3
[1] 5jic.a 1.0 0.2 0.7 0.7 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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