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AROH_BACSU_1_127

Chorismate mutase AroH

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (AROH_BACSU):D: Chorismate mutase aroH-type (57, 59, 60, 63, 73:75)
R: Substrate binding (57, 59, 60, 63, 73:75)
57, 59, 60, 63, 73:75
A2 (AROH_BACSU):D: Chorismate mutase aroH-type (7, 9, 78, 88, 90, 108, 115, 116)
R: Substrate binding (78)
7, 9, 78, 88, 90, 108, 115, 116

Full PDB list

1com, 1dbf, 1fnj, 1fnk, 2chs, 2cht, 3zo8, 3zop, 3zp4, 3zp7 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
F
5
7
A
5
9
K
6
0
R
6
3
V
7
3
T
7
4
C
7
5
R
7
E
7
8
R
9
0
Y
1
0
8
L
1
1
5
R
1
1
6
[1]1com.a pre16 . . . . . . . . . . . . .
[1]1dbf.a none . . . . . . . . . . . . .
[1]1fnj.a none . . . . . . * . . K . . .
[1]1fnk.a none . . . . . . * . . S . . .
[1]2cht.d tsa16 . . . . . . . . . . . . .
[1]3zop.a none . . . . . . . . . * . . .
[1]3zp4.c tsa16 . . . . . . . . . * . . .
[1]3zp7.b isj,pre32 . . . . . . . . . * . . .

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

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PDB.ch
A1 A2
F
5
7
A
5
9
K
6
0
R
6
3
V
7
3
T
7
4
C
7
5
R
7
A
9
E
7
8
C
8
8
R
9
0
Y
1
0
8
L
1
1
5
R
1
1
6
[1]1com.a . . . . . . . . . . . . . . .
[1]1dbf.a . . . * . . . . . . . . . . .
[1]1fnj.a . . . . . . * * . . S K . . .
[1]1fnk.a . . . . . . * . . . K S . . .
[1]2cht.d . . . . . . . . . . . . . . .
[1]3zop.a . . . . . . . . . . . * . . .
[1]3zp4.c . . . . . . . . . . . * . . .
[1]3zp7.b . . . . . . . . . . . * . . .

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
1com.a:pre
1dbf.a is apo
1fnj.a is apo
1fnk.a is apo
2cht.d:tsa
3zop.a is apo
3zp4.c:tsa
3zp7.b:isj,pre
[1] 1com.a
0
- - - 0.1 - 0.1 0.4
[1] 1dbf.a 3.1
-
- - 2.4 - 2.0 2.9
[1] 1fnj.a 0.8 -
-
- 0.9 - 0.8 1.6
[1] 1fnk.a 0.7 - -
-
0.4 - 0.5 0.9
[1] 2cht.d 0.1 - - -
0
- 0.1 0.3
[1] 3zop.a 0 - - - 0
-
0 0.1
[1] 3zp4.c 0.4 - - - 0.4 -
0.1
0.5
[1] 3zp7.b 0.1 - - - 0.1 - 0
0.3
[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
1com.a
1dbf.a
1fnj.a
1fnk.a
2cht.d
3zop.a
3zp4.c
3zp7.b
[1] 1com.a
0
.21 .08 .07 .01 .02 .04 .02
[1] 1dbf.a .21
0
.29 .25 .21 .21 .17 .19
[1] 1fnj.a .08 .29
0
.09 .09 .10 .12 .10
[1] 1fnk.a .07 .25 .09
0
.06 .06 .08 .06
[1] 2cht.d .01 .21 .09 .06
0
.01 .03 .01
[1] 3zop.a .02 .21 .10 .06 .01
0
.03 .01
[1] 3zp4.c .04 .17 .12 .08 .03 .03
0
.02
[1] 3zp7.b .02 .19 .10 .06 .01 .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
1com.a
1dbf.a
1fnj.a
1fnk.a
2cht.d
3zop.a
3zp4.c
3zp7.b
[1] 1com.a
0
0.9 0.9 1.0 0.3 0.8 0.7 0.4
[1] 1dbf.a 0.9
0
1.1 1.2 1.0 0.7 0.8 0.9
[1] 1fnj.a 0.9 1.1
0
0.5 1.1 0.8 0.6 0.8
[1] 1fnk.a 1.0 1.2 0.5
0
1.2 0.9 0.7 1.0
[1] 2cht.d 0.3 1.0 1.1 1.2
0
0.7 0.8 0.4
[1] 3zop.a 0.8 0.7 0.8 0.9 0.7
0
0.3 0.6
[1] 3zp4.c 0.7 0.8 0.6 0.7 0.8 0.3
0
0.6
[1] 3zp7.b 0.4 0.9 0.8 1.0 0.4 0.6 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
1com.a
1dbf.a
1fnj.a
1fnk.a
2cht.d
3zop.a
3zp4.c
3zp7.b
[1] 1com.a
0
2.9 1.4 1.6 0.9 2.5 2.5 1.1
[1] 1dbf.a 2.9
0
2.0 2.2 2.8 1.4 1.3 2.7
[1] 1fnj.a 1.4 2.0
0
0.7 1.4 1.2 1.4 1.3
[1] 1fnk.a 1.6 2.2 0.7
0
1.5 1.4 1.6 1.4
[1] 2cht.d 0.9 2.8 1.4 1.5
0
2.4 2.4 0.6
[1] 3zop.a 2.5 1.4 1.2 1.4 2.4
0
1.0 2.3
[1] 3zp4.c 2.5 1.3 1.4 1.6 2.4 1.0
0
2.4
[1] 3zp7.b 1.1 2.7 1.3 1.4 0.6 2.3 2.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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