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PKNB_MYCTU_2_279

Serine/threonine-protein kinase PknB [Protein kinase superfamily. Ser/Thr protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PKNB_MYCTU):D: Protein kinase (17:23, 25, 38, 40, 55, 59, 63, 72, 74, 90, 92:99, 101, 102, 138, 140, 142, 143, 145, 155:158, 178)17:23, 25, 38, 40, 55, 59, 63, 72, 74, 90, 92:99, 101, 102, 138, 140, 142, 143, 145, 155:158, 178

Full PDB list

1mru, 1o6y, 2fum, 3f61, 3f69, 3ori, 3ork, 3orl, 3orm, 3oro, 3orp, 3ort, 5u94, 6b2p (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
7
G
1
8
F
1
9
G
2
0
G
2
1
M
2
2
S
2
3
V
2
5
A
3
8
K
4
0
R
5
5
E
5
9
A
6
3
V
7
2
V
7
4
I
9
0
M
9
2
E
9
3
Y
9
4
V
9
5
D
9
6
G
9
7
T
9
9
D
1
0
2
K
1
4
0
A
1
4
2
N
1
4
3
M
1
4
5
M
1
5
5
D
1
5
6
F
1
5
7
[1]1mru.b ags,mg,mg33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1o6y.a acp,mg,mg33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2fum.a mix32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3f61.a adp,mg,mg29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3f69.b xdr35 . . . . . . . . . . . . . . . . . . . . . . . . . . . L V . .
[1]3ori.a ags,mn,mn33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3orm.a ags,mn32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3oro.a ags31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5u94.a g93,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6b2p.a cjj25 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
L
1
7
G
1
8
F
1
9
G
2
0
G
2
1
M
2
2
S
2
3
V
2
5
A
3
8
K
4
0
R
5
5
E
5
9
A
6
3
V
7
2
V
7
4
I
9
0
M
9
2
E
9
3
Y
9
4
V
9
5
D
9
6
G
9
7
V
9
8
T
9
9
R
1
0
1
D
1
0
2
D
1
3
8
K
1
4
0
A
1
4
2
N
1
4
3
M
1
4
5
M
1
5
5
D
1
5
6
F
1
5
7
G
1
5
8
G
1
7
8
[1]1mru.b . . . * * * . . . . . . . . . . * . . . . . . . . . . . . . . . . . . -
[1]1o6y.a . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . * . . -
[1]2fum.a . . * * * . . . . . . . . . . . * . . . . . . . . . . . . . . . * . . .
[1]3f61.a . . . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . -
[1]3f69.b . . . * * . . . . . . . . . . . . . . . . . . . . . . . . . L V . . . .
[1]3ori.a . . . * * * . . . . . . . . . . * . . . . . . . * . . . . . . . . . . .
[1]3orm.a . . . * * * . . . . . . . . . . * . . . . . . . . . . . . . . . . . . -
[1]3oro.a . . . . . * . . . . . . . . . . * . . . . . . . . . . . . . . . * . . .
[1]5u94.a . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . * . . .
[1]6b2p.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
1mru.b:ags,mg
1o6y.a:acp,mg
2fum.a:mix
3f61.a:adp,mg
3f69.b:xdr
3ori.a:ags,mn
3orm.a:ags,mn
3oro.a:ags
5u94.a:g93,mg
6b2p.a:cjj
[1] 1mru.b
0
2.2 0.8 1.6 0.8 0.9 0.3 1.0 0.5 0.9
[1] 1o6y.a 0.1
0.3
0.2 1.5 0.6 1.2 0.5 0.2 0.2 1.0
[1] 2fum.a 3.2 5.2
0.1
5.6 0.6 4.2 3.6 4.1 1.4 1.2
[1] 3f61.a 0.4 2.8 0.8
0.2
1.8 0.7 0.4 2.0 1.8 1.0
[1] 3f69.b 0.3 2.2 0.2 1.0
0
0.8 0.6 2.0 0.7 0.3
[1] 3ori.a 0.3 3.5 0.9 1.1 1.7
0.6
0.1 2.0 0.9 1.1
[1] 3orm.a 0.2 3.7 0.8 1.4 1.5 0.5
0.2
1.7 0.8 1.1
[1] 3oro.a 0.7 3.0 0.4 2.4 1.8 1.8 1.0
0
1.3 1.5
[1] 5u94.a 0.4 0.6 0.2 2.2 1.1 1.5 0.5 0.1
0.1
1.0
[1] 6b2p.a 0.1 0.3 0.4 0.5 0.3 0.5 0.1 0.2 0.6
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
1mru.b
1o6y.a
2fum.a
3f61.a
3f69.b
3ori.a
3orm.a
3oro.a
5u94.a
6b2p.a
[1] 1mru.b
0
.09 .20 .10 .11 .11 .11 .13 .12 .12
[1] 1o6y.a .09
0
.21 .14 .12 .17 .18 .14 .05 .07
[1] 2fum.a .20 .21
0
.20 .15 .21 .23 .29 .21 .24
[1] 3f61.a .10 .14 .20
0
.12 .10 .12 .19 .17 .17
[1] 3f69.b .11 .12 .15 .12
0
.14 .15 .22 .15 .11
[1] 3ori.a .11 .17 .21 .10 .14
0
.05 .18 .19 .19
[1] 3orm.a .11 .18 .23 .12 .15 .05
0
.14 .20 .19
[1] 3oro.a .13 .14 .29 .19 .22 .18 .14
0
.13 .18
[1] 5u94.a .12 .05 .21 .17 .15 .19 .20 .13
0
.08
[1] 6b2p.a .12 .07 .24 .17 .11 .19 .19 .18 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
1mru.b
1o6y.a
2fum.a
3f61.a
3f69.b
3ori.a
3orm.a
3oro.a
5u94.a
6b2p.a
[1] 1mru.b
0
0.8 1.3 2.3 1.9 1.3 1.2 2.1 0.8 1.2
[1] 1o6y.a 0.8
0
1.4 2.2 1.9 1.4 1.4 2.2 0.3 0.9
[1] 2fum.a 1.3 1.4
0
2.5 2.0 1.8 1.7 2.6 1.7 1.5
[1] 3f61.a 2.3 2.2 2.5
0
1.7 1.6 1.7 2.4 2.4 1.9
[1] 3f69.b 1.9 1.9 2.0 1.7
0
1.9 1.7 2.1 2.7 1.5
[1] 3ori.a 1.3 1.4 1.8 1.6 1.9
0
0.3 2.1 1.7 1.3
[1] 3orm.a 1.2 1.4 1.7 1.7 1.7 0.3
0
1.7 1.5 1.4
[1] 3oro.a 2.1 2.2 2.6 2.4 2.1 2.1 1.7
0
2.6 2.5
[1] 5u94.a 0.8 0.3 1.7 2.4 2.7 1.7 1.5 2.6
0
0.9
[1] 6b2p.a 1.2 0.9 1.5 1.9 1.5 1.3 1.4 2.5 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.7 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
1mru.b
1o6y.a
2fum.a
3f61.a
3f69.b
3ori.a
3orm.a
3oro.a
5u94.a
6b2p.a
[1] 1mru.b
0
1.0 1.6 2.6 2.1 1.8 1.7 2.4 1.1 1.4
[1] 1o6y.a 1.0
0
1.6 2.4 2.1 1.8 1.8 2.3 0.6 1.2
[1] 2fum.a 1.6 1.6
0
2.7 2.2 2.3 2.1 2.6 1.6 1.7
[1] 3f61.a 2.6 2.4 2.7
0
1.9 1.9 2.0 2.5 2.7 2.3
[1] 3f69.b 2.1 2.1 2.2 1.9
0
1.9 1.8 2.0 2.6 1.6
[1] 3ori.a 1.8 1.8 2.3 1.9 1.9
0
0.6 2.1 2.2 1.6
[1] 3orm.a 1.7 1.8 2.1 2.0 1.8 0.6
0
1.8 2.0 1.7
[1] 3oro.a 2.4 2.3 2.6 2.5 2.0 2.1 1.8
0
2.8 2.7
[1] 5u94.a 1.1 0.6 1.6 2.7 2.6 2.2 2.0 2.8
0
1.3
[1] 6b2p.a 1.4 1.2 1.7 2.3 1.6 1.6 1.7 2.7 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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