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IRIS_CATRO_24_388

Iridoid synthase [Short-chain dehydrogenases/reductases (SDR) family. Highly divergent]

Composition of the binding site

Protein chains monomer
A1 (IRIS_CATRO):109, 144:152, 178, 203, 213, 342, 345, 346, 349, 352109, 144:152, 178, 203, 213, 342, 345, 346, 349, 352
Cofactors (cF):nad/nap

Full PDB list

5coa, 5cob, 5dbf, 5dbg, 5dbi, 5dcu, 5dcw, 5dcy, 5df1, 5emh (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
G
1
4
4
I
1
4
5
K
1
4
6
F
1
4
9
F
1
5
2
Y
1
7
8
L
2
0
3
M
2
1
3
F
3
4
2
I
3
4
5
A
3
4
6
S
3
4
9
L
3
5
2
[1]5dbi.a xog12 . . . . . . . . . . . . . nad
[1]5dcu.a teg11 . . . . . . . . . . . . . nap
[1]5dcy.a none . . . . . . . . . . . . . nap
[1]5df1.a 58x12 . . . . . . . . . . . . . nap
[2]5dcw.a none . . . . . . . . . . . . .

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
W
1
0
9
G
1
4
4
I
1
4
5
K
1
4
6
H
1
4
7
Y
1
4
8
F
1
4
9
G
1
5
0
I
1
5
1
F
1
5
2
Y
1
7
8
L
2
0
3
M
2
1
3
F
3
4
2
I
3
4
5
A
3
4
6
S
3
4
9
L
3
5
2
[1]5dbi.a . . . . . . . . . . . . . . . . . . nad
[1]5dcu.a . . . . . . . . . . . . . . . . . . nap
[1]5dcy.a . . . . . . . A . . . . . . . . . . nap
[1]5df1.a . . . . . . . . . . . . . . . . . . nap
[2]5dcw.a . . . * . . * . . . . . . . . . . .

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
5dbi.a:xog
5dcu.a:teg
5dcy.a is apo
5df1.a:58x
5dcw.a is apo
[1] 5dbi.a
0
0 - 0 -
[1] 5dcu.a 0.1
0
- 0.1 -
[1] 5dcy.a 0.1 0
-
0.1 -
[1] 5df1.a 0 0 -
0
-
[2] 5dcw.a 4.2 5.0 - 3.9
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
5dbi.a
5dcu.a
5dcy.a
5df1.a
5dcw.a
[1] 5dbi.a
0
.01 .01 0 .28
[1] 5dcu.a .01
0
0 .01 .27
[1] 5dcy.a .01 0
0
.01 .27
[1] 5df1.a 0 .01 .01
0
.28
[2] 5dcw.a .28 .27 .27 .28
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.0 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
5dbi.a
5dcu.a
5dcy.a
5df1.a
5dcw.a
[1] 5dbi.a
0
0.2 1.9 0.1 3.9
[1] 5dcu.a 0.2
0
1.8 0.1 3.9
[1] 5dcy.a 1.9 1.8
0
1.9 3.9
[1] 5df1.a 0.1 0.1 1.9
0
3.9
[2] 5dcw.a 3.9 3.9 3.9 3.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.8 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
5dbi.a
5dcu.a
5dcy.a
5df1.a
5dcw.a
[1] 5dbi.a
0
0.2 3.1 0.2 5.8
[1] 5dcu.a 0.2
0
3.0 0.2 5.8
[1] 5dcy.a 3.1 3.0
0
3.0 5.8
[1] 5df1.a 0.2 0.2 3.0
0
5.7
[2] 5dcw.a 5.8 5.8 5.8 5.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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