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AROA_STRPN_1_427

3-phosphoshikimate 1-carboxyvinyltransferase [EPSP synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROA_STRPN):R: Shikimate-3-phosphate binding (20, 21)
R: Phosphoenolpyruvate binding (91:93)
25, 120, 124, 166:168, 193, 311, 312, 339, 340, 343, 384, 385
20, 21, 25, 91:93, 120, 124, 166:168, 193, 311, 312, 339, 340, 343, 384, 385

Full PDB list

1rf4, 1rf5, 1rf6, 4n3p

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
2
0
S
2
1
R
2
5
S
9
1
G
9
2
T
9
3
R
1
2
0
S
1
6
6
A
1
6
7
Q
1
6
8
R
1
9
3
I
3
1
1
D
3
1
2
K
3
3
9
E
3
4
0
R
3
4
3
H
3
8
4
R
3
8
5
[1]1rf4.c spq27 . . . . . . . . . . . . . . . . . .
[1]1rf5.a none . . . . . . . . . . . . . - - . . .
[1]1rf6.a gpj,s3p26 . . . . . . . . . . . . . . . . . .
[1]4n3p.a none S . L . . A . . N S S . . . . . . .

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
0
S
2
1
R
2
5
S
9
1
G
9
2
T
9
3
R
1
2
0
R
1
2
4
S
1
6
6
A
1
6
7
Q
1
6
8
R
1
9
3
I
3
1
1
D
3
1
2
K
3
3
9
E
3
4
0
R
3
4
3
H
3
8
4
R
3
8
5
[1]1rf4.c . . . . . . . . . . . . . . . . . . *
[1]1rf5.a . . . . . . . . . . . * . . - - . . .
[1]1rf6.a . . . . . . . . . . . . . . . . . . .
[1]4n3p.a S . L . . A . . . N S S . . . . . . .

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
1rf4.c:spq
1rf5.a is apo
1rf6.a:gpj,s3p
4n3p.a is apo
[1] 1rf4.c
0.3
- 0.7 -
[1] 1rf5.a 1.7
-
2.4 -
[1] 1rf6.a 0.3 -
0
-
[1] 4n3p.a 0.3 - 0.4
-
[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
1rf4.c
1rf5.a
1rf6.a
4n3p.a
[1] 1rf4.c
0
.17 .05 .07
[1] 1rf5.a .17
0
.14 .13
[1] 1rf6.a .05 .14
0
.04
[1] 4n3p.a .07 .13 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.5 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
1rf4.c
1rf5.a
1rf6.a
4n3p.a
[1] 1rf4.c
0
3.9 0.2 6.0
[1] 1rf5.a 3.9
0
4.0 2.1
[1] 1rf6.a 0.2 4.0
0
6.0
[1] 4n3p.a 6.0 2.1 6.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 3.0 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
1rf4.c
1rf5.a
1rf6.a
4n3p.a
[1] 1rf4.c
0
4.1 0.6 6.6
[1] 1rf5.a 4.1
0
4.1 2.8
[1] 1rf6.a 0.6 4.1
0
6.5
[1] 4n3p.a 6.6 2.8 6.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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