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ALDEC_SYNE7_10_230

Aldehyde decarbonylase [Aldehyde decarbonylase family]

Composition of the binding site

Protein chains monomer
A1 (ALDEC_SYNE7):21, 24, 25, 27, 28, 31, 32, 35, 60, 67, 87, 110, 114, 115, 117, 118, 121, 122, 125, 144, 184, 19321, 24, 25, 27, 28, 31, 32, 35, 60, 67, 87, 110, 114, 115, 117, 118, 121, 122, 125, 144, 184, 193
Metals (Me):Fe

Full PDB list

4quw, 4rc5, 4rc6, 4rc7, 4rc8 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Y
2
1
I
2
4
N
2
5
I
2
7
V
2
8
G
3
1
E
3
2
A
3
5
E
6
0
F
6
7
F
8
7
Q
1
1
0
I
1
1
4
E
1
1
5
F
1
1
7
A
1
1
8
A
1
2
1
Y
1
2
2
Y
1
2
5
V
1
8
4
M
1
9
3
[1]4rc5.a pl317 . . . . . . . . . . . . . . . . . . . . . Fe
[1]4rc6.a none . . . . . . . . . . . . . . . . . F . . . Fe
[1]4rc7.a pl317 . . . . . . . . . . Y . . . . . . . . . . Fe
[1]4rc8.a ste20 . . . . . . . . . . . . . . . . . . . . . Fe
[1]4rc8.b 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

[download in TSV format]
   
PDB.ch
A1 Me
Y
2
1
I
2
4
N
2
5
I
2
7
V
2
8
G
3
1
E
3
2
A
3
5
E
6
0
F
6
7
F
8
7
Q
1
1
0
I
1
1
4
E
1
1
5
F
1
1
7
A
1
1
8
A
1
2
1
Y
1
2
2
Y
1
2
5
E
1
4
4
V
1
8
4
M
1
9
3
[1]4rc5.a . . . . . . . . . . . . . . . . . . . . . . Fe
[1]4rc6.a . . . . . . . . . . . . . . . . . F . . . . Fe
[1]4rc7.a . . . . . . . . . . Y . . . . . . . . . . . Fe
[1]4rc8.a . . . . . . . . . . . . . . . . . . . . . . Fe
[1]4rc8.b . . . . . . . . . . . . . . . . . . . . . .

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
4rc5.a:pl3
4rc6.a is apo
4rc7.a:pl3
4rc8.a:ste
4rc8.b is apo
[1] 4rc5.a
0
- 0 0.1 -
[1] 4rc6.a 0.1
-
0.1 0.5 -
[1] 4rc7.a 0 -
0
0 -
[1] 4rc8.a 0 - 0
0
-
[1] 4rc8.b 0.5 - 0.3 0.6
-
[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
4rc5.a
4rc6.a
4rc7.a
4rc8.a
4rc8.b
[1] 4rc5.a
0
.02 0 0 .04
[1] 4rc6.a .02
0
.02 .02 .05
[1] 4rc7.a 0 .02
0
0 .03
[1] 4rc8.a 0 .02 0
0
.03
[1] 4rc8.b .04 .05 .03 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
4rc5.a
4rc6.a
4rc7.a
4rc8.a
4rc8.b
[1] 4rc5.a
0
0.3 0.2 0.2 0.8
[1] 4rc6.a 0.3
0
0.3 0.3 0.8
[1] 4rc7.a 0.2 0.3
0
0.1 0.9
[1] 4rc8.a 0.2 0.3 0.1
0
0.9
[1] 4rc8.b 0.8 0.8 0.9 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
4rc5.a
4rc6.a
4rc7.a
4rc8.a
4rc8.b
[1] 4rc5.a
0
0.7 0.5 0.5 1.1
[1] 4rc6.a 0.7
0
0.6 0.8 0.9
[1] 4rc7.a 0.5 0.6
0
0.4 1.1
[1] 4rc8.a 0.5 0.8 0.4
0
1.2
[1] 4rc8.b 1.1 0.9 1.1 1.2
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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