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AROA_AGRSC_3_453

3-phosphoshikimate 1-carboxyvinyltransferase [EPSP synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROA_AGRSC):R: Shikimate-3-phosphate binding (28, 29)
R: Phosphoenolpyruvate (98:101)
33, 55, 128, 173:175, 200, 325, 326, 353, 354, 357, 404, 405
28, 29, 33, 55, 98:101, 128, 173:175, 200, 325, 326, 353, 354, 357, 404, 405

Full PDB list

2gg4, 2gg6, 2gga, 2ggd, 2pqb, 2pqc, 2pqd

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
2
8
S
2
9
R
3
3
N
9
8
A
9
9
A
1
0
0
T
1
0
1
R
1
2
8
S
1
7
3
A
1
7
4
Q
1
7
5
R
2
0
0
I
3
2
5
D
3
2
6
K
3
5
3
E
3
5
4
R
3
5
7
H
4
0
4
R
4
0
5
[1]2gg4.a none . . . . . . . . . . . . . . . . . . .
[1]2gg6.a s3p16 . . . . . . . . . . . . . . . . . . .
[1]2gga.a gpj,s3p26 . . . . . . . . . . . . . . . . . . .
[1]2ggd.a gpj,s3p26 . . . . . G . . . . . . . . . . . . .
[1]2pqb.a gg928 . . . . . . . . . . . . . . . . . . .
[1]2pqc.a rc125 . . . . . . . . . . . . . . . . . . .
[1]2pqd.a gg928 . . . . . G . . . . . . . . . . . . .

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
8
S
2
9
R
3
3
D
5
5
N
9
8
A
9
9
A
1
0
0
T
1
0
1
R
1
2
8
S
1
7
3
A
1
7
4
Q
1
7
5
R
2
0
0
I
3
2
5
D
3
2
6
K
3
5
3
E
3
5
4
R
3
5
7
H
4
0
4
R
4
0
5
[1]2gg4.a . . . . . . . . . . . . . . . . . . . .
[1]2gg6.a . . . . . . . . . . . . . . . . . . . .
[1]2gga.a . . . . . . . . . . . . . . . . . . . .
[1]2ggd.a . . . . . . G . . . . . . . . . . . . .
[1]2pqb.a . . . . . . . . . . . . . . . . . . . .
[1]2pqc.a . . . . . . . . . . . . . . . . . . . .
[1]2pqd.a . . . . . . G . . . . . . . . . . . . .

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
2gg4.a is apo
2gg6.a:s3p
2gga.a:gpj,s3p
2ggd.a:gpj,s3p
2pqb.a:gg9
2pqc.a:rc1
2pqd.a:gg9
[1] 2gg4.a
-
0.4 0.7 0.7 0.8 0.5 0.7
[1] 2gg6.a -
0
0.2 0.6 0.5 0.4 0.5
[1] 2gga.a - 0.3
0.1
0.4 0.5 0.4 0.4
[1] 2ggd.a - 0 0.4
0.1
0.5 0.5 0.4
[1] 2pqb.a - 0.1 0.5 0.8
0
0.2 0.1
[1] 2pqc.a - 0.1 0.7 0.8 0.1
0.1
0.1
[1] 2pqd.a - 0.2 0.7 0.9 0.3 0.4
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
2gg4.a
2gg6.a
2gga.a
2ggd.a
2pqb.a
2pqc.a
2pqd.a
[1] 2gg4.a
0
.09 .07 .07 .07 .08 .09
[1] 2gg6.a .09
0
.05 .04 .03 .03 .03
[1] 2gga.a .07 .05
0
.02 .06 .06 .06
[1] 2ggd.a .07 .04 .02
0
.05 .05 .05
[1] 2pqb.a .07 .03 .06 .05
0
.01 .03
[1] 2pqc.a .08 .03 .06 .05 .01
0
.02
[1] 2pqd.a .09 .03 .06 .05 .03 .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
2gg4.a
2gg6.a
2gga.a
2ggd.a
2pqb.a
2pqc.a
2pqd.a
[1] 2gg4.a
0
6.9 6.9 6.9 6.9 6.9 6.9
[1] 2gg6.a 6.9
0
0.1 0.1 0.1 0.1 0.2
[1] 2gga.a 6.9 0.1
0
0.1 0.2 0.1 0.2
[1] 2ggd.a 6.9 0.1 0.1
0
0.2 0.2 0.2
[1] 2pqb.a 6.9 0.1 0.2 0.2
0
0.1 0.1
[1] 2pqc.a 6.9 0.1 0.1 0.2 0.1
0
0.2
[1] 2pqd.a 6.9 0.2 0.2 0.2 0.1 0.2
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
2gg4.a
2gg6.a
2gga.a
2ggd.a
2pqb.a
2pqc.a
2pqd.a
[1] 2gg4.a
0
7.2 7.2 7.3 7.3 7.3 7.4
[1] 2gg6.a 7.2
0
0.2 0.2 0.4 0.2 0.4
[1] 2gga.a 7.2 0.2
0
0.2 0.4 0.2 0.4
[1] 2ggd.a 7.3 0.2 0.2
0
0.5 0.3 0.5
[1] 2pqb.a 7.3 0.4 0.4 0.5
0
0.4 0.2
[1] 2pqc.a 7.3 0.2 0.2 0.3 0.4
0
0.3
[1] 2pqd.a 7.4 0.4 0.4 0.5 0.2 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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