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COAX_THEMA_1_246

Type III pantothenate kinase [Type III pantothenate kinase family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (COAX_THEMA):R: Substrate binding (103, 105, 106)
9, 62, 101, 102, 128, 129, 131, 145
9, 62, 101:103, 105, 106, 128, 129, 131, 145
A2 (COAX_THEMA):160, 162, 163, 179160, 162, 163, 179

Full PDB list

2gtd, 3bex, 3bf1, 3bf3 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
N
9
V
6
2
E
1
0
1
V
1
0
2
G
1
0
3
D
1
0
5
R
1
0
6
T
1
2
8
A
1
2
9
T
1
3
1
I
1
4
5
T
1
6
0
K
1
6
2
L
1
6
3
T
1
7
9
[1]2gtd.a none . . . . . . . . . . . . . . .
[1]3bex.a pau15 . . . . . . . . . . . . . . .
[1]3bf3.a paz19 . . . . . . . . . . . . . . .

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
N
9
V
6
2
E
1
0
1
V
1
0
2
G
1
0
3
D
1
0
5
R
1
0
6
T
1
2
8
A
1
2
9
T
1
3
1
I
1
4
5
T
1
6
0
K
1
6
2
L
1
6
3
T
1
7
9
[1]2gtd.a . . . . . . . . . . . . . . .
[1]3bex.a . . . . . . . . . . . . . . .
[1]3bf3.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
2gtd.a is apo
3bex.a:pau
3bf3.a:paz
[1] 2gtd.a
-
0 0
[1] 3bex.a -
0
0
[1] 3bf3.a - 0
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
2gtd.a
3bex.a
3bf3.a
[1] 2gtd.a
0
0 0
[1] 3bex.a 0
0
0
[1] 3bf3.a 0 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
2gtd.a
3bex.a
3bf3.a
[1] 2gtd.a
0
0.3 0.3
[1] 3bex.a 0.3
0
0.1
[1] 3bf3.a 0.3 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
2gtd.a
3bex.a
3bf3.a
[1] 2gtd.a
0
0.7 0.7
[1] 3bex.a 0.7
0
0.2
[1] 3bf3.a 0.7 0.2
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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