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ACON_BOVIN_28_780

Aconitate hydratase, mitochondrial [Aconitase/IPM isomerase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ACON_BOVIN):R: Substrate binding (192, 193)
R: Substrate binding (670, 671)
99, 101, 102, 128, 452, 474, 479, 607, 669
99, 101, 102, 128, 192, 193, 452, 474, 479, 607, 669:671
Cofactors (cF):sf4

Full PDB list

1aco, 1ami, 1amj, 1b0j, 1b0k, 1b0m, 1c96, 1c97, 1fgh, 1nis, 1nit, 5acn, 6acn, 7acn, 8acn (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
Q
9
9
A
1
0
1
T
1
0
2
H
1
2
8
D
1
9
2
S
1
9
3
I
4
5
2
R
4
7
4
R
4
7
9
R
6
0
7
S
6
6
9
S
6
7
0
R
6
7
1
[1]1aco.a tra12 . . . . . . . . . . . . . sf4
[1]1ami.a mic14 . . . . . . . . . . . . . sf4
[1]1b0m.a none . . . . . . . . . . . . Q sf4
[1]1c96.a none . . . . . . . . . . A . . sf4
[1]1c97.a ict13 . . . . . . . . . . A . . sf4
[1]1fgh.a ath13 . . . . . . . . . . . . . sf4
[1]1nis.a ntc13 . . . . . . . . . . . . . sf4
[1]1nit.a none . . . . . . . . . . . . . sf4
[1]7acn.a ict13 . . . . . . . . . . . . . sf4
[1]8acn.a nic13 . . . . . . . . . . . . . sf4

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 cF
Q
9
9
A
1
0
1
T
1
0
2
H
1
2
8
D
1
9
2
S
1
9
3
I
4
5
2
R
4
7
4
R
4
7
9
R
6
0
7
S
6
6
9
S
6
7
0
R
6
7
1
[1]1aco.a . . . . . . . . . . . . . sf4
[1]1ami.a . . . . . . . . . . . . . sf4
[1]1b0m.a . . . . . . . . . . . . Q sf4
[1]1c96.a . . . . . . . . . . A . . sf4
[1]1c97.a . . . . . . . . . . A . . sf4
[1]1fgh.a . . . . . . . . . . . . . sf4
[1]1nis.a . . . . . . . . . . . . . sf4
[1]1nit.a . . . . . . . . . . . . . sf4
[1]7acn.a . . . . . . . . . . . . . sf4
[1]8acn.a . . . . . . . . . . . . . sf4

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
1aco.a:tra
1ami.a:mic
1b0m.a is apo
1c96.a is apo
1c97.a:ict
1fgh.a:ath
1nis.a:ntc
1nit.a is apo
7acn.a:ict
8acn.a:nic
[1] 1aco.a
0
0.2 - - 0.2 0.1 0.2 - 0.1 0
[1] 1ami.a 0
0.1
- - 0.1 0.1 0.1 - 0 0.1
[1] 1b0m.a 0.1 0.3
-
- 0.4 0.1 0.1 - 0.1 0.2
[1] 1c96.a 0 0.2 -
-
0.1 0.1 0 - 0.2 0.1
[1] 1c97.a 0 0.3 - -
0.3
0 0.1 - 0.2 0.2
[1] 1fgh.a 0.1 0.4 - - 0.3
0
0.2 - 0.2 0.1
[1] 1nis.a 0 0.1 - - 0.2 0
0
- 0.1 0
[1] 1nit.a 0.1 0.3 - - 0.2 0.1 0.1
-
0.1 0.1
[1] 7acn.a 0 0.2 - - 0.1 0.1 0.2 -
0
0.1
[1] 8acn.a 0.1 0.3 - - 0.2 0.1 0.1 - 0.1
0.1
[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
1aco.a
1ami.a
1b0m.a
1c96.a
1c97.a
1fgh.a
1nis.a
1nit.a
7acn.a
8acn.a
[1] 1aco.a
0
.02 .03 .03 .04 .02 .03 .02 .01 .02
[1] 1ami.a .02
0
.05 .03 .04 .03 .05 .03 .01 .03
[1] 1b0m.a .03 .05
0
.05 .01 .03 .03 .03 .04 .03
[1] 1c96.a .03 .03 .05
0
.04 .02 .02 .02 .02 .02
[1] 1c97.a .04 .04 .01 .04
0
.04 .04 .04 .03 .04
[1] 1fgh.a .02 .03 .03 .02 .04
0
.02 0 .02 0
[1] 1nis.a .03 .05 .03 .02 .04 .02
0
.02 .04 .02
[1] 1nit.a .02 .03 .03 .02 .04 0 .02
0
.02 0
[1] 7acn.a .01 .01 .04 .02 .03 .02 .04 .02
0
.02
[1] 8acn.a .02 .03 .03 .02 .04 0 .02 0 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1aco.a
1ami.a
1b0m.a
1c96.a
1c97.a
1fgh.a
1nis.a
1nit.a
7acn.a
8acn.a
[1] 1aco.a
0
0.2 0.4 0.2 0.3 0.2 0.2 0.2 0.1 0.2
[1] 1ami.a 0.2
0
0.3 0.3 0.3 0.3 0.2 0.2 0.2 0.3
[1] 1b0m.a 0.4 0.3
0
0.4 0.4 0.5 0.3 0.3 0.5 0.5
[1] 1c96.a 0.2 0.3 0.4
0
0.3 0.2 0.3 0.3 0.3 0.2
[1] 1c97.a 0.3 0.3 0.4 0.3
0
0.3 0.3 0.3 0.3 0.3
[1] 1fgh.a 0.2 0.3 0.5 0.2 0.3
0
0.3 0.3 0.2 0.1
[1] 1nis.a 0.2 0.2 0.3 0.3 0.3 0.3
0
0.1 0.3 0.3
[1] 1nit.a 0.2 0.2 0.3 0.3 0.3 0.3 0.1
0
0.3 0.3
[1] 7acn.a 0.1 0.2 0.5 0.3 0.3 0.2 0.3 0.3
0
0.2
[1] 8acn.a 0.2 0.3 0.5 0.2 0.3 0.1 0.3 0.3 0.2
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
1aco.a
1ami.a
1b0m.a
1c96.a
1c97.a
1fgh.a
1nis.a
1nit.a
7acn.a
8acn.a
[1] 1aco.a
0
0.2 0.6 0.7 0.7 0.2 0.2 0.4 0.2 0.3
[1] 1ami.a 0.2
0
0.5 0.7 0.7 0.3 0.2 0.4 0.2 0.3
[1] 1b0m.a 0.6 0.5
0
0.8 0.8 0.6 0.5 0.4 0.6 0.7
[1] 1c96.a 0.7 0.7 0.8
0
0.6 0.7 0.7 0.7 0.7 0.7
[1] 1c97.a 0.7 0.7 0.8 0.6
0
0.7 0.7 0.8 0.7 0.7
[1] 1fgh.a 0.2 0.3 0.6 0.7 0.7
0
0.3 0.4 0.2 0.2
[1] 1nis.a 0.2 0.2 0.5 0.7 0.7 0.3
0
0.3 0.3 0.3
[1] 1nit.a 0.4 0.4 0.4 0.7 0.8 0.4 0.3
0
0.4 0.4
[1] 7acn.a 0.2 0.2 0.6 0.7 0.7 0.2 0.3 0.4
0
0.2
[1] 8acn.a 0.3 0.3 0.7 0.7 0.7 0.2 0.3 0.4 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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