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DHAK_ECOLI_1_356

PEP-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DHAK_ECOLI):D: DhaK (52, 53, 56, 78:80, 104, 106, 108, 109, 143, 218)
R: Dihydroxyacetone binding (53, 56)
52, 53, 56, 78:80, 104, 106, 108, 109, 143, 218

Full PDB list

1oi2, 1oi3, 1uod, 1uoe, 3pnk, 3pnl, 3pnm, 3pno, 3pnq, 4lrx, 4lry (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
5
2
G
5
3
H
5
6
F
7
8
T
7
9
S
8
0
K
1
0
4
Y
1
0
6
G
1
0
8
D
1
0
9
H
2
1
8
[1]1oi2.a none . . . . . . . . . . .
[1]1oi3.a none . . . . . . . . . . .
[1]1uod.a g3h10 . . . . . . . . . . *
[1]3pnm.a none . . A . . . . . . . .
[1]3pno.a none . . N . . . . . . . .
[1]3pnq.d 2ha6 . . N . . . . . . . .
[1]4lry.a none . . . . L . . . . . .

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
5
2
G
5
3
H
5
6
F
7
8
T
7
9
S
8
0
K
1
0
4
Y
1
0
6
G
1
0
8
D
1
0
9
Y
1
4
3
H
2
1
8
[1]1oi2.a . . . . . . . . . . . *
[1]1oi3.a . . . . . . . . . . . .
[1]1uod.a . . . . . . . . . . . *
[1]3pnm.a . . A . . . . . . . . .
[1]3pno.a . . N . . . . . . . . .
[1]3pnq.d . . N . . . . . . . . .
[1]4lry.a . . . . L . . . . . . .

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
1oi2.a is apo
1oi3.a is apo
1uod.a:g3h
3pnm.a is apo
3pno.a is apo
3pnq.d:2ha
4lry.a is apo
[1] 1oi2.a
-
- 0.8 - - 0.2 -
[1] 1oi3.a -
-
0.6 - - 0.1 -
[1] 1uod.a - -
0.8
- - 0.1 -
[1] 3pnm.a - - 0.7
-
- 0.2 -
[1] 3pno.a - - 0.7 -
-
0.2 -
[1] 3pnq.d - - 0.7 - -
0.1
-
[1] 4lry.a - - 0.5 - - 0.2
-
[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
1oi2.a
1oi3.a
1uod.a
3pnm.a
3pno.a
3pnq.d
4lry.a
[1] 1oi2.a
0
.02 .01 .04 .03 .03 .04
[1] 1oi3.a .02
0
.02 .03 .04 .03 .02
[1] 1uod.a .01 .02
0
.03 .03 .02 .03
[1] 3pnm.a .04 .03 .03
0
.03 .03 .02
[1] 3pno.a .03 .04 .03 .03
0
.01 .03
[1] 3pnq.d .03 .03 .02 .03 .01
0
.03
[1] 4lry.a .04 .02 .03 .02 .03 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1oi2.a
1oi3.a
1uod.a
3pnm.a
3pno.a
3pnq.d
4lry.a
[1] 1oi2.a
0
0.3 0.1 0.4 0.3 0.4 0.3
[1] 1oi3.a 0.3
0
0.2 0.3 0.3 0.3 0.3
[1] 1uod.a 0.1 0.2
0
0.4 0.3 0.3 0.3
[1] 3pnm.a 0.4 0.3 0.4
0
0.3 0.3 0.4
[1] 3pno.a 0.3 0.3 0.3 0.3
0
0.2 0.3
[1] 3pnq.d 0.4 0.3 0.3 0.3 0.2
0
0.3
[1] 4lry.a 0.3 0.3 0.3 0.4 0.3 0.3
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
1oi2.a
1oi3.a
1uod.a
3pnm.a
3pno.a
3pnq.d
4lry.a
[1] 1oi2.a
0
0.5 0.1 0.7 0.5 0.7 0.6
[1] 1oi3.a 0.5
0
0.4 0.6 0.4 0.6 0.5
[1] 1uod.a 0.1 0.4
0
0.6 0.5 0.6 0.5
[1] 3pnm.a 0.7 0.6 0.6
0
0.5 0.6 0.5
[1] 3pno.a 0.5 0.4 0.5 0.5
0
0.4 0.4
[1] 3pnq.d 0.7 0.6 0.6 0.6 0.4
0
0.5
[1] 4lry.a 0.6 0.5 0.5 0.5 0.4 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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