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DHQSD_ARATH_90_603_SDH

Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DHQSD_ARATH):R: Shikimate dehydrogenase (328, 336, 338, 379:381, 385, 406, 423, 550)
575, 578, 582
328, 336, 338, 379:381, 385, 406, 423, 550, 575, 578, 582

Full PDB list

2gpt, 2o7q, 2o7s, 6bmb (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
3
2
8
S
3
3
6
S
3
3
8
S
3
7
9
T
3
8
1
K
3
8
5
N
4
0
6
D
4
2
3
Y
5
5
0
F
5
7
5
Q
5
7
8
Q
5
8
2
[1]2gpt.a skm12 . . . . . . . . . . . .
[1]2o7q.a dhk12 . . . . . . . . . . . .
[1]6bmb.a skm12 . . . . 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
I
3
2
8
S
3
3
6
S
3
3
8
S
3
7
9
C
3
8
0
T
3
8
1
K
3
8
5
N
4
0
6
D
4
2
3
Y
5
5
0
F
5
7
5
Q
5
7
8
Q
5
8
2
[1]2gpt.a . . . . . . . . . . . . .
[1]2o7q.a . . . . . . . . . . . . .
[1]6bmb.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
2gpt.a:skm
2o7q.a:dhk
6bmb.a:skm
[1] 2gpt.a
0.1
0.1 0.1
[1] 2o7q.a 0.1
0.2
0.1
[1] 6bmb.a 0.1 0.2
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
2gpt.a
2o7q.a
6bmb.a
[1] 2gpt.a
0
.02 .02
[1] 2o7q.a .02
0
.02
[1] 6bmb.a .02 .02
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
2gpt.a
2o7q.a
6bmb.a
[1] 2gpt.a
0
0.1 0.2
[1] 2o7q.a 0.1
0
0.2
[1] 6bmb.a 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2gpt.a
2o7q.a
6bmb.a
[1] 2gpt.a
0
0.2 0.4
[1] 2o7q.a 0.2
0
0.4
[1] 6bmb.a 0.4 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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