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AROA_ECOLI_3_240

3-phosphoshikimate 1-carboxyvinyltransferase [EPSP synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROA_ECOLI):R: Shikimate-3-phosphate binding (22, 23)
R: Phosphoenolpyruvate (94:97)
R: Shikimate-3-phosphate binding (169:171)
27, 124, 197, 200, 313, 336, 340, 341, 344, 385, 386, 411
22, 23, 27, 94:97, 124, 169:171, 197, 200, 313, 336, 340, 341, 344, 385, 386, 411

Full PDB list

1g6s, 1g6t, 1mi4, 1q36, 1x8r, 1x8t, 2aa9, 2aay, 2pq9, 2qfq, 2qfs, 2qft, 2qfu, 3fjx, 3fjz, 3fk0, 3fk1 (redundant Pocketome entry); 1eps (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
2
2
S
2
3
R
2
7
N
9
4
G
9
6
T
9
7
R
1
2
4
S
1
6
9
S
1
7
0
Q
1
7
1
S
1
9
7
Y
2
0
0
D
3
1
3
N
3
3
6
K
3
4
0
E
3
4
1
R
3
4
4
H
3
8
5
R
3
8
6
K
4
1
1
[1]1g6s.a gpj,s3p26 . . . . . . . . . . . . . . . . . . . .
[1]1mi4.a s3p16 . . . . A . . . . . . . . . . . . . . .
[1]1q36.a skp26 . . . . . . . . . . . . A . . . . . . .
[1]1x8r.a sc125 . . . . . . . . . . . . . . . . . . . .
[1]1x8t.a rc125 . . . . . . . . . . . . . . . . . . . .
[1]2aa9.a skm12 . . . . . . . . . . . . . . . . . . . .
[1]2aay.a gpj,skm22 . . . . . . . . . . . . . . . . . . . .
[1]2pq9.a gg928 . . . . . . . . . . . . . . . . . . . .
[1]2qfs.a s3p16 . . . . . . . . . . . . . . . . . . . .
[1]3fjz.a gpf,s3p26 . . . . . I . . . . . . . . . . . . . .
[1]3fk0.a s3p16 . . . . . I . . . . . . . . . . . . . .

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
K
2
2
S
2
3
R
2
7
N
9
4
A
9
5
G
9
6
T
9
7
R
1
2
4
S
1
6
9
S
1
7
0
Q
1
7
1
S
1
9
7
Y
2
0
0
D
3
1
3
N
3
3
6
K
3
4
0
E
3
4
1
R
3
4
4
H
3
8
5
R
3
8
6
K
4
1
1
[1]1g6s.a . . . . . . . . . . . . . . . . * . . . .
[1]1mi4.a . . . . . A . . . . . . . . . . * . . . .
[1]1q36.a . . . . . . . . . . . . . A . . * . . . .
[1]1x8r.a . . . . . . . . . . . . . . . . . . . . .
[1]1x8t.a . . . . . . . . . . . . . . . . . . . . .
[1]2aa9.a . . . . . . . . . . . . . . . . * . . . .
[1]2aay.a . . . . . . . . . . . . . . . . * . . . .
[1]2pq9.a . . . . . . . . . . . . . . . . . . . . .
[1]2qfs.a . . . . . . . . . . . . . . . . * . . . .
[1]3fjz.a . . . . . . I . . . . . . . . . * . . . .
[1]3fk0.a . . . . . . I . . . . . . . . . * . . . .

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
1g6s.a:gpj,s3p
1mi4.a:s3p
1q36.a:skp
1x8r.a:sc1
1x8t.a:rc1
2aa9.a:skm
2aay.a:gpj,skm
2pq9.a:gg9
2qfs.a:s3p
3fjz.a:gpf,s3p
3fk0.a:s3p
[1] 1g6s.a
0
0.1 0.2 0.6 1.0 0.1 0 0.4 0 0.1 0.1
[1] 1mi4.a 0.6
0
0.1 0.9 1.0 0 0.5 0.8 0.1 0.6 0.1
[1] 1q36.a 0.8 0.1
0
0.6 1.0 0 0.4 0.5 0 0.8 0
[1] 1x8r.a 1.1 0.2 0.1
0.2
0.2 0.1 0.7 0.3 0 0.9 0.1
[1] 1x8t.a 0.7 0.2 0.2 0.2
0
0.1 0.6 0.2 0.2 0.7 0.1
[1] 2aa9.a 0.7 0.2 0.4 1.0 1.6
0
0.4 0.8 0.2 0.7 0.2
[1] 2aay.a 0.3 0.1 0.3 0.9 1.3 0.1
0.2
0.7 0.1 0.4 0.2
[1] 2pq9.a 1.1 0.1 0 0.2 0 0 0.7
0.1
0 0.8 0
[1] 2qfs.a 0.4 0 0.2 0.8 1.0 0 0.2 0.9
0
0.3 0
[1] 3fjz.a 0.2 0.2 0.1 0.6 1.0 0 0.1 0.5 0
0.1
0.1
[1] 3fk0.a 0.7 0.2 0.2 1.0 1.5 0.1 0.4 0.7 0.1 0.6
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
1g6s.a
1mi4.a
1q36.a
1x8r.a
1x8t.a
2aa9.a
2aay.a
2pq9.a
2qfs.a
3fjz.a
3fk0.a
[1] 1g6s.a
0
.03 .05 .09 .08 .05 .03 .10 .02 0 .04
[1] 1mi4.a .03
0
.05 .10 .09 .06 .05 .11 .03 .03 .04
[1] 1q36.a .05 .05
0
.06 .07 .06 .06 .07 .04 .05 .05
[1] 1x8r.a .09 .10 .06
0
.04 .10 .10 .01 .09 .09 .09
[1] 1x8t.a .08 .09 .07 .04
0
.11 .10 .04 .10 .09 .10
[1] 2aa9.a .05 .06 .06 .10 .11
0
.02 .10 .04 .05 .03
[1] 2aay.a .03 .05 .06 .10 .10 .02
0
.10 .03 .03 .03
[1] 2pq9.a .10 .11 .07 .01 .04 .10 .10
0
.10 .10 .10
[1] 2qfs.a .02 .03 .04 .09 .10 .04 .03 .10
0
.02 .04
[1] 3fjz.a 0 .03 .05 .09 .09 .05 .03 .10 .02
0
.04
[1] 3fk0.a .04 .04 .05 .09 .10 .03 .03 .10 .04 .04
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
1g6s.a
1mi4.a
1q36.a
1x8r.a
1x8t.a
2aa9.a
2aay.a
2pq9.a
2qfs.a
3fjz.a
3fk0.a
[1] 1g6s.a
0
0.2 0.2 0.3 0.7 0.2 0.2 0.3 0.2 0.1 0.4
[1] 1mi4.a 0.2
0
0.2 0.3 0.6 0.2 0.2 0.3 0.2 0.2 0.4
[1] 1q36.a 0.2 0.2
0
0.2 0.6 0.2 0.2 0.2 0.2 0.2 0.4
[1] 1x8r.a 0.3 0.3 0.2
0
0.6 0.3 0.3 0.2 0.3 0.3 0.5
[1] 1x8t.a 0.7 0.6 0.6 0.6
0
0.6 0.7 0.6 0.7 0.7 0.7
[1] 2aa9.a 0.2 0.2 0.2 0.3 0.6
0
0.1 0.3 0.3 0.2 0.4
[1] 2aay.a 0.2 0.2 0.2 0.3 0.7 0.1
0
0.3 0.3 0.2 0.4
[1] 2pq9.a 0.3 0.3 0.2 0.2 0.6 0.3 0.3
0
0.4 0.3 0.5
[1] 2qfs.a 0.2 0.2 0.2 0.3 0.7 0.3 0.3 0.4
0
0.2 0.2
[1] 3fjz.a 0.1 0.2 0.2 0.3 0.7 0.2 0.2 0.3 0.2
0
0.3
[1] 3fk0.a 0.4 0.4 0.4 0.5 0.7 0.4 0.4 0.5 0.2 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
1g6s.a
1mi4.a
1q36.a
1x8r.a
1x8t.a
2aa9.a
2aay.a
2pq9.a
2qfs.a
3fjz.a
3fk0.a
[1] 1g6s.a
0
0.2 0.2 0.6 1.2 0.5 0.4 0.8 0.2 0.3 0.5
[1] 1mi4.a 0.2
0
0.2 0.6 1.2 0.4 0.3 0.8 0.2 0.4 0.4
[1] 1q36.a 0.2 0.2
0
0.6 1.2 0.4 0.4 0.8 0.2 0.3 0.4
[1] 1x8r.a 0.6 0.6 0.6
0
1.1 0.7 0.7 0.5 0.6 0.7 0.7
[1] 1x8t.a 1.2 1.2 1.2 1.1
0
1.2 1.3 1.1 1.2 1.2 1.3
[1] 2aa9.a 0.5 0.4 0.4 0.7 1.2
0
0.2 0.9 0.4 0.5 0.5
[1] 2aay.a 0.4 0.3 0.4 0.7 1.3 0.2
0
0.8 0.4 0.4 0.5
[1] 2pq9.a 0.8 0.8 0.8 0.5 1.1 0.9 0.8
0
0.8 0.9 0.9
[1] 2qfs.a 0.2 0.2 0.2 0.6 1.2 0.4 0.4 0.8
0
0.3 0.4
[1] 3fjz.a 0.3 0.4 0.3 0.7 1.2 0.5 0.4 0.9 0.3
0
0.5
[1] 3fk0.a 0.5 0.4 0.4 0.7 1.3 0.5 0.5 0.9 0.4 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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