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AROA_COXBU_1_438

3-phosphoshikimate 1-carboxyvinyltransferase [EPSP synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROA_COXBU):R: Shikimate-3-phosphate binding (21)
R: Phosphoenolpyruvate (95, 96)
123, 169, 315, 342, 343, 346, 386, 387
21, 95, 96, 123, 169, 315, 342, 343, 346, 386, 387
Cofactors (cF):s3p/skm

Full PDB list

3roi, 3slh, 3tr1, 4egr, 4gfp, 4znd (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
K
2
1
G
9
5
T
9
6
R
1
2
3
Q
1
6
9
D
3
1
5
E
3
4
3
R
3
4
6
H
3
8
6
R
3
8
7
[1]3slh.a gpj10 . . . . . . . . . . s3p,skm
[1]3tr1.a none . . . . . . . . . .
[1]4egr.a pep10 . . . . . . . . . .

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
K
2
1
G
9
5
T
9
6
R
1
2
3
Q
1
6
9
D
3
1
5
K
3
4
2
E
3
4
3
R
3
4
6
H
3
8
6
R
3
8
7
[1]3slh.a . . . . . . . . . . . s3p,skm
[1]3tr1.a . . . . . . . . . . .
[1]4egr.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
3slh.a:gpj
3tr1.a is apo
4egr.a:pep
[1] 3slh.a
0
- 0.1
[1] 3tr1.a 0.8
-
0.2
[1] 4egr.a 0.6 -
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
3slh.a
3tr1.a
4egr.a
[1] 3slh.a
0
.08 .06
[1] 3tr1.a .08
0
.02
[1] 4egr.a .06 .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
3slh.a
3tr1.a
4egr.a
[1] 3slh.a
0
0.4 0.3
[1] 3tr1.a 0.4
0
0.3
[1] 4egr.a 0.3 0.3
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
3slh.a
3tr1.a
4egr.a
[1] 3slh.a
0
0.6 0.4
[1] 3tr1.a 0.6
0
0.5
[1] 4egr.a 0.4 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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