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CLCA_RHOOP_1_257

Chlorocatechol 1,2-dioxygenase [Intradiol ring-cleavage dioxygenase family]

Composition of the binding site

Protein chains monomer
A1 (CLCA_RHOOP):49, 52, 53, 74, 76:78, 134, 169, 171, 191, 194, 196, 210, 22449, 52, 53, 74, 76:78, 134, 169, 171, 191, 194, 196, 210, 224
Metals (Me):Fe

Full PDB list

1s9a, 3o32, 3o5u, 3o6j, 3o6r

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
L
4
9
D
5
2
A
5
3
I
7
4
G
7
6
P
7
7
F
7
8
Y
1
3
4
Y
1
6
9
I
1
7
1
R
1
9
1
H
1
9
4
H
1
9
6
C
2
2
4
[1]1s9a.a bez9 . . . . . . . . . . . . . . Fe
[1]3o32.a 35c10 . . . . . . . . . . . . . . Fe
[1]3o5u.a dhb11 . . . . . . . . . . . . . . Fe
[1]3o6j.a hqn9 . . . . . . . . . . . . . . Fe
[1]3o6j.b none . . . . . . . . . . . . . . Fe
[1]3o6r.a pyg9 . . . . . . . . . . . . . . Fe

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 Me
L
4
9
D
5
2
A
5
3
I
7
4
G
7
6
P
7
7
F
7
8
Y
1
3
4
Y
1
6
9
I
1
7
1
R
1
9
1
H
1
9
4
H
1
9
6
Q
2
1
0
C
2
2
4
[1]1s9a.a . . . . . . . . * . . . . . . Fe
[1]3o32.a . . . . . . . . . . . . . . . Fe
[1]3o5u.a . . . . . . . . . . . . . . . Fe
[1]3o6j.a . . . . . . . . . . . . . . . Fe
[1]3o6j.b . . . . . . . . . . . . . . . Fe
[1]3o6r.a . . . . . . . . . . . . . . . Fe

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
1s9a.a:bez
3o32.a:35c
3o5u.a:dhb
3o6j.a:hqn
3o6j.b is apo
3o6r.a:pyg
[1] 1s9a.a
0.1
1.1 1.2 0.8 - 1.1
[1] 3o32.a 0.2
0.3
0.1 0.2 - 0.2
[1] 3o5u.a 0.2 0.3
0
0.2 - 0.2
[1] 3o6j.a 0.2 0.8 0.2
0.2
- 0.5
[1] 3o6j.b 0.4 0.2 0.4 0.4
-
0.5
[1] 3o6r.a 0.1 0.8 0.4 0.2 -
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
1s9a.a
3o32.a
3o5u.a
3o6j.a
3o6j.b
3o6r.a
[1] 1s9a.a
0
.09 .09 .05 .11 .07
[1] 3o32.a .09
0
.01 .05 .06 .07
[1] 3o5u.a .09 .01
0
.06 .05 .08
[1] 3o6j.a .05 .05 .06
0
.08 .03
[1] 3o6j.b .11 .06 .05 .08
0
.09
[1] 3o6r.a .07 .07 .08 .03 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1s9a.a
3o32.a
3o5u.a
3o6j.a
3o6j.b
3o6r.a
[1] 1s9a.a
0
0.3 0.5 0.3 0.5 0.3
[1] 3o32.a 0.3
0
0.5 0.2 0.5 0.3
[1] 3o5u.a 0.5 0.5
0
0.5 0.6 0.5
[1] 3o6j.a 0.3 0.2 0.5
0
0.5 0.3
[1] 3o6j.b 0.5 0.5 0.6 0.5
0
0.5
[1] 3o6r.a 0.3 0.3 0.5 0.3 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1s9a.a
3o32.a
3o5u.a
3o6j.a
3o6j.b
3o6r.a
[1] 1s9a.a
0
1.0 1.1 0.9 0.9 0.9
[1] 3o32.a 1.0
0
0.7 0.5 0.7 0.6
[1] 3o5u.a 1.1 0.7
0
0.6 0.9 0.6
[1] 3o6j.a 0.9 0.5 0.6
0
0.8 0.4
[1] 3o6j.b 0.9 0.7 0.9 0.8
0
0.9
[1] 3o6r.a 0.9 0.6 0.6 0.4 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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