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CYC1_STRCO_1_361

Epi-isozizaene synthase [Terpene synthase family]

Composition of the binding site

Protein chains monomer
A1 (CYC1_STRCO):69, 72, 73, 92, 95, 96, 99, 172, 192:199, 203, 240, 325, 329, 332, 333, 33969, 72, 73, 92, 95, 96, 99, 172, 192:199, 203, 240, 325, 329, 332, 333, 339
Metals (Me):Mg

Full PDB list

3kb9, 3kbk, 3lg5, 3lgk, 4ltv, 4ltz, 4luu, 4lxw, 4lz0, 4lz3, 4lzc, 6ax9, 6axm, 6axn, 6axo, 6axu (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
L
7
2
M
7
3
S
9
2
F
9
5
F
9
6
D
9
9
Y
1
7
2
R
1
9
4
T
1
9
7
F
1
9
8
A
1
9
9
W
2
0
3
N
2
4
0
W
3
2
5
V
3
2
9
F
3
3
2
H
3
3
3
Y
3
3
9
[1]3kb9.a btm14 . . . . . . . . . . . . . . . . . . Mg
[1]3lg5.a btm14 . . . . . . . . . A . . . . . . . . Mg
[1]3lgk.a none . . . . . N . . . . . . . . . . . -
[1]4ltz.a btm14 . . . M . . . . . . . . . . . . . . Mg
[1]4luu.a btm14 . . . . . . . . . . . . . . A . . . Mg
[1]4lxw.a btm14 V . . . . . . . . . . . . . . . . . Mg
[1]4lz3.a btm14 . . . H . . . . . . . . . . . . . . Mg
[1]4lzc.a none . . . . . . . . . . . . . F . . . . Mg
[1]6ax9.a btm14 . . . N . . . . . . . . . . . . . . Mg
[1]6axm.a btm14 . . . Y . . . . . . . . . . . . . . Mg
[1]6axn.a btm14 . . . C . . . . . . . . . . . . . . Mg
[1]6axo.a none . . . . S . . . . . . . . . . . . -
[1]6axu.a btm14 . . . . . . . . . . . Y . . . . . . Mg
[2]3kbk.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 Me
Y
6
9
L
7
2
M
7
3
S
9
2
F
9
5
F
9
6
D
9
9
Y
1
7
2
E
1
9
2
L
1
9
3
R
1
9
4
R
1
9
5
L
1
9
6
T
1
9
7
F
1
9
8
A
1
9
9
W
2
0
3
N
2
4
0
W
3
2
5
V
3
2
9
F
3
3
2
H
3
3
3
Y
3
3
9
[1]3kb9.a . . . . . . . . . . . . . . * . . . . . . . . Mg
[1]3lg5.a . . . . . . . . . . . . . . A . . . . . . . . Mg
[1]3lgk.a . . . . . . N . . . . . . . * . . . . . . . -
[1]4ltz.a . . . . M . . . . . . . . . * . . . . . . . . Mg
[1]4luu.a . . . . . . . . . . . . . . * . . . . A . . . Mg
[1]4lxw.a . V . . . . . . . . . . . . * . . . . . . . . Mg
[1]4lz3.a . . . . H . . . . . . . . . * . . . . . . . . Mg
[1]4lzc.a . . . . . . . . . . . . . . * . . . F . . . . Mg
[1]6ax9.a . . . . N . . . . . . . . . . . . . . . . . . Mg
[1]6axm.a . . . . Y . . . . . . . . . * . . . . . . . . Mg
[1]6axn.a . . . . C . . . . . . . . . * . . . . . . . . Mg
[1]6axo.a . . . . . S . . . . . . . . * . . . . . . . -
[1]6axu.a . . . . . . . . . . . . . . * . Y . . . . . . Mg
[2]3kbk.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
3kb9.a:btm
3lg5.a:btm
3lgk.a is apo
4ltz.a:btm
4luu.a:btm
4lxw.a:btm
4lz3.a:btm
4lzc.a is apo
6ax9.a:btm
6axm.a:btm
6axn.a:btm
6axo.a is apo
6axu.a:btm
3kbk.a is apo
[1] 3kb9.a
0
1.2 - 0 0 0.1 0 - 0.4 0 0.2 - 0 -
[1] 3lg5.a 0.2
0
- 0.1 0.2 0.3 0.2 - 0.6 0.1 0.7 - 0.2 -
[1] 3lgk.a 0.6 1.6
-
0.6 0.5 0.5 0.4 - 1.0 0.5 0.9 - 0.7 -
[1] 4ltz.a 0 1.2 -
0
0 0.1 0 - 0.1 0 0 - 0 -
[1] 4luu.a 0 1.2 - 0
0
0.1 0 - 0.3 0.1 0.2 - 0 -
[1] 4lxw.a 0.1 1.4 - 0.1 0
0
0 - 0.5 0 0.2 - 0 -
[1] 4lz3.a 0 1.1 - 0 0 0.1
0
- 0.4 0.1 0.2 - 0 -
[1] 4lzc.a 0 1.2 - 0 0 0.1 0
-
0.4 0 0.2 - 0 -
[1] 6ax9.a 0 0.9 - 0 0 0.1 0 -
0
0 0 - 0 -
[1] 6axm.a 0 1.1 - 0 0 0.1 0 - 0.2
0
0.8 - 0.2 -
[1] 6axn.a 0 1.1 - 0 0 0.1 0 - 0.3 0
0
- 0 -
[1] 6axo.a 0 1.1 - 0 0 0.1 0 - 0.4 0 0.2
-
0.1 -
[1] 6axu.a 0 1.0 - 0 0 0.1 0 - 0.5 0 0.2 -
0
-
[2] 3kbk.a 8.3 7.5 - 8.1 8.3 7.3 7.8 - 6.9 8.3 7.4 - 7.3
-
[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
3kb9.a
3lg5.a
3lgk.a
4ltz.a
4luu.a
4lxw.a
4lz3.a
4lzc.a
6ax9.a
6axm.a
6axn.a
6axo.a
6axu.a
3kbk.a
[1] 3kb9.a
0
.08 .06 .02 0 .02 .01 .01 .03 .03 .01 .01 .01 .46
[1] 3lg5.a .08
0
.07 .09 .08 .09 .07 .08 .07 .05 .08 .07 .07 .45
[1] 3lgk.a .06 .07
0
.07 .06 .06 .05 .06 .07 .03 .06 .05 .07 .51
[1] 4ltz.a .02 .09 .07
0
.02 .02 .02 .01 .02 .04 .01 .02 .03 .46
[1] 4luu.a 0 .08 .06 .02
0
.03 .01 .01 .03 .04 .02 .01 .02 .46
[1] 4lxw.a .02 .09 .06 .02 .03
0
.03 .01 .04 .05 .03 .02 .03 .46
[1] 4lz3.a .01 .07 .05 .02 .01 .03
0
.01 .03 .03 .02 0 .03 .46
[1] 4lzc.a .01 .08 .06 .01 .01 .01 .01
0
.03 .03 .02 .01 .02 .46
[1] 6ax9.a .03 .07 .07 .02 .03 .04 .03 .03
0
.05 .02 .03 .04 .44
[1] 6axm.a .03 .05 .03 .04 .04 .05 .03 .03 .05
0
.04 .03 .05 .49
[1] 6axn.a .01 .08 .06 .01 .02 .03 .02 .02 .02 .04
0
.01 .03 .47
[1] 6axo.a .01 .07 .05 .02 .01 .02 0 .01 .03 .03 .01
0
.02 .46
[1] 6axu.a .01 .07 .07 .03 .02 .03 .03 .02 .04 .05 .03 .02
0
.47
[2] 3kbk.a .46 .45 .51 .46 .46 .46 .46 .46 .44 .49 .47 .46 .47
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
3kb9.a
3lg5.a
3lgk.a
4ltz.a
4luu.a
4lxw.a
4lz3.a
4lzc.a
6ax9.a
6axm.a
6axn.a
6axo.a
6axu.a
3kbk.a
[1] 3kb9.a
0
0.1 0.8 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.1 0.5 0.1 5.9
[1] 3lg5.a 0.1
0
0.8 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.1 0.6 0.1 5.8
[1] 3lgk.a 0.8 0.8
0
0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.6 0.8 5.8
[1] 4ltz.a 0.1 0.1 0.8
0
0.2 0.1 0.1 0.2 0.2 0.2 0.2 0.6 0.2 5.9
[1] 4luu.a 0.1 0.1 0.8 0.2
0
0.1 0.1 0.2 0.2 0.2 0.2 0.6 0.1 5.8
[1] 4lxw.a 0.1 0.1 0.8 0.1 0.1
0
0.2 0.2 0.2 0.2 0.2 0.6 0.2 5.9
[1] 4lz3.a 0.1 0.1 0.8 0.1 0.1 0.2
0
0.2 0.2 0.2 0.1 0.5 0.1 5.9
[1] 4lzc.a 0.2 0.2 0.8 0.2 0.2 0.2 0.2
0
0.2 0.2 0.2 0.5 0.2 5.9
[1] 6ax9.a 0.2 0.2 0.8 0.2 0.2 0.2 0.2 0.2
0
0.2 0.2 0.5 0.2 5.9
[1] 6axm.a 0.2 0.2 0.8 0.2 0.2 0.2 0.2 0.2 0.2
0
0.1 0.5 0.2 5.9
[1] 6axn.a 0.1 0.1 0.8 0.2 0.2 0.2 0.1 0.2 0.2 0.1
0
0.5 0.2 5.9
[1] 6axo.a 0.5 0.6 0.6 0.6 0.6 0.6 0.5 0.5 0.5 0.5 0.5
0
0.6 5.9
[1] 6axu.a 0.1 0.1 0.8 0.2 0.1 0.2 0.1 0.2 0.2 0.2 0.2 0.6
0
5.8
[2] 3kbk.a 5.9 5.8 5.8 5.9 5.8 5.9 5.9 5.9 5.9 5.9 5.9 5.9 5.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
3kb9.a
3lg5.a
3lgk.a
4ltz.a
4luu.a
4lxw.a
4lz3.a
4lzc.a
6ax9.a
6axm.a
6axn.a
6axo.a
6axu.a
3kbk.a
[1] 3kb9.a
0
0.4 1.5 0.3 0.3 0.3 0.2 0.4 0.3 0.5 0.1 1.1 0.6 7.2
[1] 3lg5.a 0.4
0
1.5 0.5 0.3 0.5 0.4 0.5 0.3 0.5 0.3 1.1 0.6 7.2
[1] 3lgk.a 1.5 1.5
0
1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.1 1.6 7.0
[1] 4ltz.a 0.3 0.5 1.5
0
0.4 0.3 0.3 0.4 0.3 0.5 0.3 1.0 0.6 7.3
[1] 4luu.a 0.3 0.3 1.5 0.4
0
0.4 0.4 0.5 0.3 0.5 0.2 1.1 0.6 7.2
[1] 4lxw.a 0.3 0.5 1.5 0.3 0.4
0
0.4 0.4 0.4 0.6 0.3 1.1 0.7 7.3
[1] 4lz3.a 0.2 0.4 1.5 0.3 0.4 0.4
0
0.4 0.2 0.5 0.2 1.0 0.6 7.3
[1] 4lzc.a 0.4 0.5 1.5 0.4 0.5 0.4 0.4
0
0.4 0.6 0.4 1.1 0.7 7.3
[1] 6ax9.a 0.3 0.3 1.5 0.3 0.3 0.4 0.2 0.4
0
0.5 0.3 1.0 0.6 6.8
[1] 6axm.a 0.5 0.5 1.5 0.5 0.5 0.6 0.5 0.6 0.5
0
0.4 1.0 0.4 6.6
[1] 6axn.a 0.1 0.3 1.5 0.3 0.2 0.3 0.2 0.4 0.3 0.4
0
1.0 0.5 7.0
[1] 6axo.a 1.1 1.1 1.1 1.0 1.1 1.1 1.0 1.1 1.0 1.0 1.0
0
1.1 6.5
[1] 6axu.a 0.6 0.6 1.6 0.6 0.6 0.7 0.6 0.7 0.6 0.4 0.5 1.1
0
6.8
[2] 3kbk.a 7.2 7.2 7.0 7.3 7.2 7.3 7.3 7.3 6.8 6.6 7.0 6.5 6.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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