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ARIS_ASPTE_10_320

Aristolochene synthase [Terpene synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ARIS_ASPTE):R: Substrate-binding (314, 315)
63, 67, 83, 86:88, 90, 153, 157, 175, 178:181, 183, 184, 215, 219, 220, 223, 226, 227, 305, 308
63, 67, 83, 86:88, 90, 153, 157, 175, 178:181, 183, 184, 215, 219, 220, 223, 226, 227, 305, 308, 314, 315
Metals (Me):Mg

Full PDB list

2e4o, 2oa6, 3bnx, 3bny, 3cke, 4kux, 4kvd, 4kvi, 4kvw, 4kvy, 4kwd, 5imi, 5imn, 5imp, 5in8, 5ivg (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
V
6
3
Y
6
7
L
8
3
L
8
6
F
8
7
D
9
0
F
1
5
3
R
1
7
5
V
1
7
9
G
1
8
0
K
1
8
1
L
1
8
3
L
1
8
4
L
2
1
5
N
2
1
9
S
2
2
3
K
2
2
6
E
2
2
7
N
3
0
5
W
3
0
8
R
3
1
4
Y
3
1
5
[1]2oa6.d none . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4kux.b fps24 . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4kvd.d 1ss15 . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4kvi.a 1sv14 . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4kvw.a jf415 . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4kvy.a jf115 . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4kwd.a jf215 . . . . . . . . . . . . . . . . . . . . . . Mg
[1]5imp.b jf115 . . . . . . . . . . . . . . . . . . A . . . Mg
[1]5in8.b none . . . . . . . . . . . . . . . . . . . . . . Mg
[1]5ivg.b fps24 . . . . . . . . . . . . . . . . . . A . . . Mg
[2]3bnx.b fpp24 . . . . . . . . . . . . . . . . . . . . . .
[2]3bny.d fpf25 . . . . . . . . . . . . . . . . . . . . . . Mg
[2]3cke.a fdf26 . . . . . . . . . . . . . . . . . . . . . .

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 Me
V
6
3
Y
6
7
L
8
3
L
8
6
F
8
7
L
8
8
D
9
0
F
1
5
3
Q
1
5
7
R
1
7
5
D
1
7
8
V
1
7
9
G
1
8
0
K
1
8
1
L
1
8
3
L
1
8
4
L
2
1
5
N
2
1
9
D
2
2
0
S
2
2
3
K
2
2
6
E
2
2
7
N
3
0
5
W
3
0
8
R
3
1
4
Y
3
1
5
[1]2oa6.d . . . . . . . . . . . . . . . . . * . . . . . . . . Mg
[1]4kux.b . * . . . . . . . * . . . . . . . * . . . . . . . . Mg
[1]4kvd.d . . . . . . . . . . . . . . . . . * . . . . . . . . Mg
[1]4kvi.a . * . . . . . . . * . . . . . . . * . . . . . . . . Mg
[1]4kvw.a . . . . . . . . . * . . . . . . . * . . . . . . . . Mg
[1]4kvy.a . . . . . . . . . . . . . . . . . * . . . . . . . . Mg
[1]4kwd.a . * . . . . . . . . . . . . . . . * . . . . . . . . Mg
[1]5imp.b . * . . . . . . . . . . . . . . . * . . . . A . . . Mg
[1]5in8.b . * . . . . . . H . . . . . . . . * . . . . . . . . Mg
[1]5ivg.b . * . . . . . . . * . . . . . . . * . . . . A . . . Mg
[2]3bnx.b . . . . . . . . . . . . . . . . . . . . . . . . * .
[2]3bny.d . * . . . . . . . . . . . . . . . * . . . . . . * . Mg
[2]3cke.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
2oa6.d is apo
4kux.b:fps
4kvd.d:1ss
4kvi.a:1sv
4kvw.a:jf4
4kvy.a:jf1
4kwd.a:jf2
5imp.b:jf1
5in8.b is apo
5ivg.b:fps
3bnx.b:fpp
3bny.d:fpf
3cke.a:fdf
[1] 2oa6.d
-
1.3 0.3 0.2 0.3 0 0.5 0.4 - 1.1 1.5 1.8 2.1
[1] 4kux.b -
0
0.4 0.1 0.1 0.1 0.4 0.7 - 0.1 2.3 2.2 2.0
[1] 4kvd.d - 0.6
0
0 0 0 0.3 0.4 - 0.5 1.8 1.2 1.8
[1] 4kvi.a - 0.5 0.2
0
0 0 0.4 0.7 - 0.5 2.1 1.9 2.2
[1] 4kvw.a - 0.2 0.1 0
0
0 0.4 0.4 - 0.3 2.1 1.3 1.7
[1] 4kvy.a - 0.4 0.1 0 0
0
0.4 0.4 - 0.4 2.0 1.1 1.7
[1] 4kwd.a - 1.0 0.2 0.1 0.3 1.1
0
0.1 - 0.9 2.3 1.6 2.7
[1] 5imp.b - 1.7 0.5 0.2 0.5 1.1 0
0
- 1.8 2.3 1.5 2.9
[1] 5in8.b - 1.2 0.3 0.2 0.7 0.6 0.5 1.0
-
1.3 2.3 2.1 2.1
[1] 5ivg.b - 0 0.3 0.1 0 0.2 0.5 0.7 -
0
2.4 2.0 2.2
[2] 3bnx.b - 2.6 0.1 0.1 0.1 0.3 0.3 0.4 - 3.1
0.1
1.1 0.1
[2] 3bny.d - 2.4 0.2 0.2 0.5 1.5 0.1 0.2 - 2.7 1.6
0.3
1.0
[2] 3cke.a - 3.3 0.1 0.2 0.1 0.3 0.2 0.5 - 3.7 0.2 1.1
0
[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
2oa6.d
4kux.b
4kvd.d
4kvi.a
4kvw.a
4kvy.a
4kwd.a
5imp.b
5in8.b
5ivg.b
3bnx.b
3bny.d
3cke.a
[1] 2oa6.d
0
.17 .09 .17 .12 .11 .07 .05 .23 .18 .23 .21 .26
[1] 4kux.b .17
0
.10 .02 .07 .08 .17 .19 .07 .01 .28 .22 .31
[1] 4kvd.d .09 .10
0
.08 .06 .05 .11 .12 .15 .10 .24 .19 .27
[1] 4kvi.a .17 .02 .08
0
.07 .08 .15 .17 .06 .03 .28 .20 .30
[1] 4kvw.a .12 .07 .06 .07
0
.01 .13 .15 .12 .07 .24 .19 .27
[1] 4kvy.a .11 .08 .05 .08 .01
0
.12 .13 .13 .08 .24 .18 .27
[1] 4kwd.a .07 .17 .11 .15 .13 .12
0
.02 .22 .17 .28 .21 .31
[1] 5imp.b .05 .19 .12 .17 .15 .13 .02
0
.23 .19 .27 .20 .30
[1] 5in8.b .23 .07 .15 .06 .12 .13 .22 .23
0
.07 .28 .21 .29
[1] 5ivg.b .18 .01 .10 .03 .07 .08 .17 .19 .07
0
.29 .22 .32
[2] 3bnx.b .23 .28 .24 .28 .24 .24 .28 .27 .28 .29
0
.15 .04
[2] 3bny.d .21 .22 .19 .20 .19 .18 .21 .20 .21 .22 .15
0
.17
[2] 3cke.a .26 .31 .27 .30 .27 .27 .31 .30 .29 .32 .04 .17
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
2oa6.d
4kux.b
4kvd.d
4kvi.a
4kvw.a
4kvy.a
4kwd.a
5imp.b
5in8.b
5ivg.b
3bnx.b
3bny.d
3cke.a
[1] 2oa6.d
0
0.8 0.4 0.6 0.4 0.4 0.2 0.3 1.1 0.8 2.5 2.1 2.5
[1] 4kux.b 0.8
0
0.5 0.3 0.5 0.5 0.8 0.9 0.5 0.1 2.8 2.2 2.7
[1] 4kvd.d 0.4 0.5
0
0.3 0.2 0.2 0.3 0.5 0.8 0.5 2.5 2.0 2.5
[1] 4kvi.a 0.6 0.3 0.3
0
0.2 0.2 0.6 0.7 0.5 0.3 2.7 2.1 2.6
[1] 4kvw.a 0.4 0.5 0.2 0.2
0
0.1 0.4 0.5 0.7 0.5 2.6 2.0 2.5
[1] 4kvy.a 0.4 0.5 0.2 0.2 0.1
0
0.4 0.5 0.7 0.5 2.6 2.0 2.5
[1] 4kwd.a 0.2 0.8 0.3 0.6 0.4 0.4
0
0.2 1.1 0.8 2.5 2.0 2.4
[1] 5imp.b 0.3 0.9 0.5 0.7 0.5 0.5 0.2
0
1.2 0.9 2.4 2.1 2.4
[1] 5in8.b 1.1 0.5 0.8 0.5 0.7 0.7 1.1 1.2
0
0.5 2.9 2.2 2.8
[1] 5ivg.b 0.8 0.1 0.5 0.3 0.5 0.5 0.8 0.9 0.5
0
2.8 2.2 2.7
[2] 3bnx.b 2.5 2.8 2.5 2.7 2.6 2.6 2.5 2.4 2.9 2.8
0
1.4 0.2
[2] 3bny.d 2.1 2.2 2.0 2.1 2.0 2.0 2.0 2.1 2.2 2.2 1.4
0
1.3
[2] 3cke.a 2.5 2.7 2.5 2.6 2.5 2.5 2.4 2.4 2.8 2.7 0.2 1.3
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
2oa6.d
4kux.b
4kvd.d
4kvi.a
4kvw.a
4kvy.a
4kwd.a
5imp.b
5in8.b
5ivg.b
3bnx.b
3bny.d
3cke.a
[1] 2oa6.d
0
0.9 0.6 0.7 0.7 0.7 0.7 0.7 1.2 0.9 2.9 2.4 2.8
[1] 4kux.b 0.9
0
0.6 0.4 0.5 0.5 0.8 1.0 0.7 0.3 3.1 2.5 3.0
[1] 4kvd.d 0.6 0.6
0
0.5 0.3 0.4 0.6 0.7 0.9 0.6 2.9 2.4 2.9
[1] 4kvi.a 0.7 0.4 0.5
0
0.4 0.4 0.7 0.8 0.7 0.5 3.0 2.4 3.0
[1] 4kvw.a 0.7 0.5 0.3 0.4
0
0.2 0.6 0.7 0.8 0.5 3.0 2.4 2.9
[1] 4kvy.a 0.7 0.5 0.4 0.4 0.2
0
0.5 0.7 0.9 0.6 3.0 2.4 2.9
[1] 4kwd.a 0.7 0.8 0.6 0.7 0.6 0.5
0
0.4 1.2 0.9 2.9 2.4 2.8
[1] 5imp.b 0.7 1.0 0.7 0.8 0.7 0.7 0.4
0
1.3 0.9 2.9 2.5 2.8
[1] 5in8.b 1.2 0.7 0.9 0.7 0.8 0.9 1.2 1.3
0
0.7 3.2 2.5 3.2
[1] 5ivg.b 0.9 0.3 0.6 0.5 0.5 0.6 0.9 0.9 0.7
0
3.1 2.5 3.1
[2] 3bnx.b 2.9 3.1 2.9 3.0 3.0 3.0 2.9 2.9 3.2 3.1
0
1.7 0.6
[2] 3bny.d 2.4 2.5 2.4 2.4 2.4 2.4 2.4 2.5 2.5 2.5 1.7
0
1.5
[2] 3cke.a 2.8 3.0 2.9 3.0 2.9 2.9 2.8 2.8 3.2 3.1 0.6 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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