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DEOC_ECOLI_1_258

Deoxyribose-phosphate aldolase [DeoC/FbaB aldolase family. DeoC type 2 subfamily]

Composition of the binding site

Protein chains monomer
A1 (DEOC_ECOLI):16, 18, 20, 47, 71, 73, 100, 102, 137, 139, 166:172, 201, 203:205, 207, 235:23816, 18, 20, 47, 71, 73, 100, 102, 137, 139, 166:172, 201, 203:205, 207, 235:238

Full PDB list

1jcj, 1jcl, 1ktn, 1p1x, 3npu, 3npv, 3npw, 3npx, 3nq2, 3nq8, 3nqv, 3nr0, 3q2d, 5eky, 5el1, 5emu (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
D
1
6
T
1
8
L
2
0
C
4
7
A
7
1
V
7
3
E
1
0
0
D
1
0
2
K
1
3
7
I
1
3
9
K
1
6
7
S
1
6
9
T
1
7
0
G
1
7
1
K
2
0
1
A
2
0
3
G
2
0
4
G
2
0
5
G
2
3
6
A
2
3
7
S
2
3
8
[1]3npu.a none H A - Y W S G A S . V . . . I . . . . . .
[1]3npv.a none H A A Y W S G A S . V . . . I . . . . . .
[1]3npw.b none H A - F W S G A S . V . . . I . . . . . .
[1]3npx.a none H A A F W S G A S . V . . . I . . . . . .
[1]3nq2.a none H A A F W S G A S . V . . . I V . . . . .
[1]3nq8.a ben9 H A S F C S G A S . V . . . I V . . . . .
[1]3nqv.a ben9 H A - F C S S A A . T T P . I V . . . . .
[1]3nr0.a none H A - F C S S A A . V . . . I V . . . . .
[1]3q2d.a 3ny12 H A S F C S S A A . V . . . I V . . . . .
[1]3q2d.b 3ny12 - - - F C S S A A . V . . . I V . . . . .
[2]1jcj.a hpd12 . . . . . . . . . . * . . . L . . . . . .
[2]1jcl.a hpd13 . . . . . . . . . . * . . . . . . . . . .
[2]1p1x.a none . . . . . . . . . . . . . . . . . . . . .
[2]5eky.a bu26 . . . . . . . . . . * . . . . . . . . . .
[2]5el1.a none . . . . . . . . . . . . . . . . . . . . .

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
D
1
6
T
1
8
L
2
0
C
4
7
A
7
1
V
7
3
E
1
0
0
D
1
0
2
K
1
3
7
I
1
3
9
I
1
6
6
K
1
6
7
T
1
6
8
S
1
6
9
T
1
7
0
G
1
7
1
K
1
7
2
K
2
0
1
A
2
0
3
G
2
0
4
G
2
0
5
R
2
0
7
F
2
3
5
G
2
3
6
A
2
3
7
S
2
3
8
[1]3npu.a H A - Y W S G A S . . V . . . . . I . . . . * . . .
[1]3npv.a H A A Y W S G A S . . V . . . . . I . . . . * . . .
[1]3npw.b H A - F W S G A S . . V . . . . . I . . . . . . . .
[1]3npx.a H A A F W S G A S . . V . . . . . I . . . . . . . .
[1]3nq2.a H A A F W S G A S . . V . . . . . I V . . . . . . .
[1]3nq8.a H A S F C S G A S . . V . . . . . I V . . . . . . .
[1]3nqv.a H A - F C S S A A . V T S T P . . I V . . . . . . .
[1]3nr0.a H A - F C S S A A . . V . . . . . I V . . . . . . .
[1]3q2d.a H A S F C S S A A . . V . . . . . I V . . . . . . .
[1]3q2d.b - - - F C S S A A . . V . . . . . I V . . . . . . .
[2]1jcj.a . . . . . . . * * . . * . . . . . L . . . . . . . .
[2]1jcl.a . . . . . . . * * . . * . . . . . * . . . . . . . .
[2]1p1x.a . . . . . . . * * . . * . . . . . * . . . . . . . .
[2]5eky.a * . . . . . . * * . . * . . . . . * . . . . . . . .
[2]5el1.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
3npu.a is apo
3npv.a is apo
3npw.b is apo
3npx.a is apo
3nq2.a is apo
3nq8.a:ben
3nqv.a:ben
3nr0.a is apo
3q2d.a:3ny
3q2d.b:3ny
1jcj.a:hpd
1jcl.a:hpd
1p1x.a is apo
5eky.a:bu2
5el1.a is apo
[1] 3npu.a
-
- - - - 1.4 1.2 - 2.1 1.5 1.4 2.0 - 1.4 -
[1] 3npv.a -
-
- - - 1.6 1.4 - 2.4 2.3 1.2 1.9 - 1.2 -
[1] 3npw.b - -
-
- - 0.1 1.2 - 2.0 0.4 0.2 0.7 - 0.5 -
[1] 3npx.a - - -
-
- 0.3 0.8 - 2.0 0.6 0.3 0.9 - 0.8 -
[1] 3nq2.a - - - -
-
0.2 1.1 - 2.0 0.5 0.6 1.3 - 1.3 -
[1] 3nq8.a - - - - -
0
0.3 - 1.1 0.1 0.2 1.0 - 0.9 -
[1] 3nqv.a - - - - - 1.7
0.2
- 0.3 0.7 3.5 3.8 - 2.4 -
[1] 3nr0.a - - - - - 0 0.1
-
0.4 0 0.3 1.0 - 1.2 -
[1] 3q2d.a - - - - - 0 0.3 -
0.2
0 0.4 1.0 - 1.2 -
[1] 3q2d.b - - - - - 0 0.1 - 0.1
0
0.4 1.1 - 1.2 -
[2] 1jcj.a - - - - - 2.2 4.0 - 5.2 3.0
0.6
0.6 - 0.8 -
[2] 1jcl.a - - - - - 3.1 4.9 - 5.9 3.9 0.6
0.6
- 0.8 -
[2] 1p1x.a - - - - - 3.0 4.8 - 5.8 4.1 0.6 0.7
-
0.8 -
[2] 5eky.a - - - - - 3.3 4.7 - 6.1 4.1 0.7 0.7 -
0.8
-
[2] 5el1.a - - - - - 3.1 4.9 - 6.0 4.0 0.7 0.5 - 0.8
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
3npu.a
3npv.a
3npw.b
3npx.a
3nq2.a
3nq8.a
3nqv.a
3nr0.a
3q2d.a
3q2d.b
1jcj.a
1jcl.a
1p1x.a
5eky.a
5el1.a
[1] 3npu.a
0
.04 .10 .09 .10 .12 .25 .10 .11 .11 .31 .33 .32 .34 .33
[1] 3npv.a .04
0
.11 .11 .13 .13 .28 .14 .14 .15 .31 .33 .33 .35 .34
[1] 3npw.b .10 .11
0
.01 .03 .07 .22 .09 .09 .10 .25 .27 .27 .27 .27
[1] 3npx.a .09 .11 .01
0
.02 .07 .23 .08 .08 .09 .26 .28 .27 .28 .28
[1] 3nq2.a .10 .13 .03 .02
0
.06 .23 .07 .07 .08 .28 .30 .30 .30 .30
[1] 3nq8.a .12 .13 .07 .07 .06
0
.18 .03 .03 .04 .22 .25 .24 .25 .24
[1] 3nqv.a .25 .28 .22 .23 .23 .18
0
.17 .15 .16 .36 .38 .38 .39 .38
[1] 3nr0.a .10 .14 .09 .08 .07 .03 .17
0
.02 .02 .25 .27 .27 .29 .28
[1] 3q2d.a .11 .14 .09 .08 .07 .03 .15 .02
0
.01 .25 .28 .27 .28 .27
[1] 3q2d.b .11 .15 .10 .09 .08 .04 .16 .02 .01
0
.27 .29 .28 .30 .28
[2] 1jcj.a .31 .31 .25 .26 .28 .22 .36 .25 .25 .27
0
.07 .07 .07 .07
[2] 1jcl.a .33 .33 .27 .28 .30 .25 .38 .27 .28 .29 .07
0
.01 .02 0
[2] 1p1x.a .32 .33 .27 .27 .30 .24 .38 .27 .27 .28 .07 .01
0
.02 0
[2] 5eky.a .34 .35 .27 .28 .30 .25 .39 .29 .28 .30 .07 .02 .02
0
.02
[2] 5el1.a .33 .34 .27 .28 .30 .24 .38 .28 .27 .28 .07 0 0 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
3npu.a
3npv.a
3npw.b
3npx.a
3nq2.a
3nq8.a
3nqv.a
3nr0.a
3q2d.a
3q2d.b
1jcj.a
1jcl.a
1p1x.a
5eky.a
5el1.a
[1] 3npu.a
0
0.2 1.6 1.6 1.9 1.7 2.5 1.8 1.8 1.9 1.7 1.7 1.5 1.6 1.6
[1] 3npv.a 0.2
0
1.6 2.0 2.2 1.8 2.5 1.8 2.3 1.9 1.6 1.6 1.5 1.5 1.5
[1] 3npw.b 1.6 1.6
0
0.3 0.9 0.6 2.2 0.9 0.9 0.9 0.7 0.7 0.5 0.5 0.5
[1] 3npx.a 1.6 2.0 0.3
0
0.9 1.0 2.1 0.8 0.9 0.9 1.6 1.6 1.5 1.5 1.5
[1] 3nq2.a 1.9 2.2 0.9 0.9
0
1.1 2.0 0.5 0.7 0.5 1.7 1.7 1.6 1.7 1.6
[1] 3nq8.a 1.7 1.8 0.6 1.0 1.1
0
2.1 0.6 1.1 0.6 1.1 1.1 0.9 1.0 1.0
[1] 3nqv.a 2.5 2.5 2.2 2.1 2.0 2.1
0
2.0 2.0 2.1 2.3 2.3 2.1 2.1 2.1
[1] 3nr0.a 1.8 1.8 0.9 0.8 0.5 0.6 2.0
0
0.2 0.2 1.1 1.1 0.8 0.8 0.7
[1] 3q2d.a 1.8 2.3 0.9 0.9 0.7 1.1 2.0 0.2
0
0.2 1.9 1.9 1.8 1.8 1.8
[1] 3q2d.b 1.9 1.9 0.9 0.9 0.5 0.6 2.1 0.2 0.2
0
1.1 1.1 0.9 0.8 0.8
[2] 1jcj.a 1.7 1.6 0.7 1.6 1.7 1.1 2.3 1.1 1.9 1.1
0
0.1 0.5 0.6 0.6
[2] 1jcl.a 1.7 1.6 0.7 1.6 1.7 1.1 2.3 1.1 1.9 1.1 0.1
0
0.5 0.6 0.6
[2] 1p1x.a 1.5 1.5 0.5 1.5 1.6 0.9 2.1 0.8 1.8 0.9 0.5 0.5
0
0.2 0.2
[2] 5eky.a 1.6 1.5 0.5 1.5 1.7 1.0 2.1 0.8 1.8 0.8 0.6 0.6 0.2
0
0.1
[2] 5el1.a 1.6 1.5 0.5 1.5 1.6 1.0 2.1 0.7 1.8 0.8 0.6 0.6 0.2 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
3npu.a
3npv.a
3npw.b
3npx.a
3nq2.a
3nq8.a
3nqv.a
3nr0.a
3q2d.a
3q2d.b
1jcj.a
1jcl.a
1p1x.a
5eky.a
5el1.a
[1] 3npu.a
0
0.4 2.4 2.4 2.6 2.5 3.5 2.6 2.6 2.7 2.6 2.6 2.5 2.5 2.5
[1] 3npv.a 0.4
0
2.4 2.6 2.8 2.6 3.5 2.6 2.9 2.8 2.5 2.5 2.4 2.5 2.5
[1] 3npw.b 2.4 2.4
0
0.5 1.0 0.8 2.7 0.9 0.9 0.9 0.8 0.8 0.6 0.6 0.6
[1] 3npx.a 2.4 2.6 0.5
0
0.9 1.0 2.7 0.9 0.9 0.9 1.7 1.6 1.5 1.6 1.6
[1] 3nq2.a 2.6 2.8 1.0 0.9
0
1.2 2.6 0.7 0.8 0.7 1.8 1.8 1.7 1.8 1.8
[1] 3nq8.a 2.5 2.6 0.8 1.0 1.2
0
2.8 0.7 0.9 0.7 1.4 1.2 1.2 1.3 1.3
[1] 3nqv.a 3.5 3.5 2.7 2.7 2.6 2.8
0
2.5 2.5 2.6 2.9 2.9 2.8 2.8 2.8
[1] 3nr0.a 2.6 2.6 0.9 0.9 0.7 0.7 2.5
0
0.3 0.3 1.2 1.1 1.0 0.9 0.8
[1] 3q2d.a 2.6 2.9 0.9 0.9 0.8 0.9 2.5 0.3
0
0.3 1.8 1.8 1.7 1.7 1.7
[1] 3q2d.b 2.7 2.8 0.9 0.9 0.7 0.7 2.6 0.3 0.3
0
1.2 1.1 1.0 0.9 0.9
[2] 1jcj.a 2.6 2.5 0.8 1.7 1.8 1.4 2.9 1.2 1.8 1.2
0
0.5 0.7 0.7 0.7
[2] 1jcl.a 2.6 2.5 0.8 1.6 1.8 1.2 2.9 1.1 1.8 1.1 0.5
0
0.6 0.8 0.8
[2] 1p1x.a 2.5 2.4 0.6 1.5 1.7 1.2 2.8 1.0 1.7 1.0 0.7 0.6
0
0.7 0.7
[2] 5eky.a 2.5 2.5 0.6 1.6 1.8 1.3 2.8 0.9 1.7 0.9 0.7 0.8 0.7
0
0.1
[2] 5el1.a 2.5 2.5 0.6 1.6 1.8 1.3 2.8 0.8 1.7 0.9 0.7 0.8 0.7 0.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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