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BPPS_SALOF_50_598

(+)-bornyl diphosphate synthase, chloroplastic [Terpene synthase family]

Composition of the binding site

Protein chains monomer
A1 (BPPS_SALOF):314, 323, 344, 347, 348, 351, 355, 426, 451:453, 457, 492, 493, 496, 500, 501, 504, 512, 564, 572, 578314, 323, 344, 347, 348, 351, 355, 426, 451:453, 457, 492, 493, 496, 500, 501, 504, 512, 564, 572, 578
Metals (Me):Mg

Full PDB list

1n1b, 1n1z, 1n20, 1n21, 1n22, 1n23, 1n24 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
R
3
1
4
W
3
2
3
I
3
4
4
A
3
4
7
T
3
4
8
D
3
5
1
D
3
5
5
Y
4
2
6
V
4
5
2
A
4
5
3
I
4
5
7
L
4
9
2
R
4
9
3
D
4
9
6
T
5
0
0
S
5
0
1
E
5
0
4
K
5
1
2
Y
5
7
2
F
5
7
8
[1]1n1b.b none . . . . . . . . . . . . . . . - - . . . Mg
[1]1n1z.a btb14 . . . . . . . . . . . . . . . . . . . . Mg
[1]1n20.a 3ag19 . . . . . . . . . . . . . . . . . . . . Mg
[1]1n22.a 7a810 . . . . . . . . . . . . . . . . . . . . Mg
[1]1n22.b 7a8,mg11 . . . . . . . . . . . . . . . . . . . - Mg
[1]1n23.a 2bn10 . . . . . . . . . . . . . . . . . . . . Mg
[1]1n24.a bp219 . . . . . . . . . . . . . . . . . . . . Mg

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 Me
R
3
1
4
W
3
2
3
I
3
4
4
A
3
4
7
T
3
4
8
D
3
5
1
D
3
5
5
Y
4
2
6
S
4
5
1
V
4
5
2
A
4
5
3
I
4
5
7
L
4
9
2
R
4
9
3
D
4
9
6
T
5
0
0
S
5
0
1
E
5
0
4
K
5
1
2
I
5
6
4
Y
5
7
2
F
5
7
8
[1]1n1b.b . . . . . . . . . . . . . . . . - - . . . . Mg
[1]1n1z.a . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1n20.a . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1n22.a . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1n22.b . . . . . . . . . . . . . . . . . . . . . - Mg
[1]1n23.a . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1n24.a . . . . . . . . . . . . . . . . . . . . . . Mg

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
1n1b.b is apo
1n1z.a:btb
1n20.a:3ag
1n22.a:7a8
1n22.b:7a8,mg
1n23.a:2bn
1n24.a:bp2
[1] 1n1b.b
-
0 0.1 0 0.1 0 0.1
[1] 1n1z.a -
0
0.2 0 0.4 0.1 0.2
[1] 1n20.a - 0.1
0
0 0.3 0 0.1
[1] 1n22.a - 0.1 0.2
0
0.5 0 0
[1] 1n22.b - 0.1 0.2 0
0.2
0 0
[1] 1n23.a - 0 0.2 0 0.4
0
0.1
[1] 1n24.a - 0 0.2 0 0.4 0
0
[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
1n1b.b
1n1z.a
1n20.a
1n22.a
1n22.b
1n23.a
1n24.a
[1] 1n1b.b
0
.03 .03 .04 .03 .03 .03
[1] 1n1z.a .03
0
.01 .02 .03 0 .02
[1] 1n20.a .03 .01
0
.02 .04 .01 .02
[1] 1n22.a .04 .02 .02
0
.02 .01 .01
[1] 1n22.b .03 .03 .04 .02
0
.03 .03
[1] 1n23.a .03 0 .01 .01 .03
0
.01
[1] 1n24.a .03 .02 .02 .01 .03 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
1n1b.b
1n1z.a
1n20.a
1n22.a
1n22.b
1n23.a
1n24.a
[1] 1n1b.b
0
1.0 1.1 1.1 1.0 1.0 1.0
[1] 1n1z.a 1.0
0
0.2 0.1 1.7 0.1 0.2
[1] 1n20.a 1.1 0.2
0
0.2 1.7 0.2 0.2
[1] 1n22.a 1.1 0.1 0.2
0
1.7 0.2 0.1
[1] 1n22.b 1.0 1.7 1.7 1.7
0
1.7 1.7
[1] 1n23.a 1.0 0.1 0.2 0.2 1.7
0
0.1
[1] 1n24.a 1.0 0.2 0.2 0.1 1.7 0.1
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
1n1b.b
1n1z.a
1n20.a
1n22.a
1n22.b
1n23.a
1n24.a
[1] 1n1b.b
0
1.4 1.4 1.4 2.0 1.4 1.4
[1] 1n1z.a 1.4
0
0.2 0.1 2.4 0.2 0.2
[1] 1n20.a 1.4 0.2
0
0.2 2.3 0.2 0.2
[1] 1n22.a 1.4 0.1 0.2
0
2.4 0.2 0.2
[1] 1n22.b 2.0 2.4 2.3 2.4
0
2.4 2.4
[1] 1n23.a 1.4 0.2 0.2 0.2 2.4
0
0.2
[1] 1n24.a 1.4 0.2 0.2 0.2 2.4 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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