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AROE_CORGL_1_283

Quinate/shikimate dehydrogenase (NAD(+)) [Shikimate dehydrogenase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROE_CORGL):R: Quinate/shikimate binding (17, 19)
9, 67, 69, 73, 94, 110, 258
9, 17, 19, 67, 69, 73, 94, 110, 258
Cofactors (cF):nad

Full PDB list

2nlo, 3jyo, 3jyp, 3jyq (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
L
9
S
1
7
T
1
9
N
6
7
T
6
9
K
7
3
N
9
4
D
1
1
0
Q
2
5
8
[1]3jyo.a none . . . . . . . . . nad
[1]3jyp.a qic13 . . . . . . . . . nad
[1]3jyq.a skm12 . . . . . . . . . nad

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

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PDB.ch
A1 cF
L
9
S
1
7
T
1
9
N
6
7
T
6
9
K
7
3
N
9
4
D
1
1
0
Q
2
5
8
[1]3jyo.a . . . . . . . . . nad
[1]3jyp.a . . . . . . . . . nad
[1]3jyq.a . . . . . . . . . nad

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
3jyo.a is apo
3jyp.a:qic
3jyq.a:skm
[1] 3jyo.a
-
0.4 0.1
[1] 3jyp.a -
0
0
[1] 3jyq.a - 0.1
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
3jyo.a
3jyp.a
3jyq.a
[1] 3jyo.a
0
.04 .03
[1] 3jyp.a .04
0
.01
[1] 3jyq.a .03 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
3jyo.a
3jyp.a
3jyq.a
[1] 3jyo.a
0
0.2 0.2
[1] 3jyp.a 0.2
0
0.1
[1] 3jyq.a 0.2 0.1
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

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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
3jyo.a
3jyp.a
3jyq.a
[1] 3jyo.a
0
0.4 0.5
[1] 3jyp.a 0.4
0
0.3
[1] 3jyq.a 0.5 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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