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DCMC_HUMAN_38_492

Malonyl-CoA decarboxylase, mitochondrial

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DCMC_HUMAN):R: Catalytic domain (218, 291:293, 300:305, 329, 330, 419, 422, 423, 425)
R: Malonyl-CoA binding (300:305)
218, 291:293, 300:305, 329, 330, 419, 422, 423, 425

Full PDB list

2ygw, 4f0x (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
I
2
9
1
S
2
9
2
L
2
9
3
G
3
0
0
V
3
0
1
E
3
0
2
G
3
0
4
T
3
0
5
S
3
2
9
P
3
3
0
V
4
1
9
F
4
2
2
H
4
2
3
[1]4f0x.a none . . . . . . . . . . . . .
[1]4f0x.d 0or23 . . . . . . . . . . . . .

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
V
2
1
8
I
2
9
1
S
2
9
2
L
2
9
3
G
3
0
0
V
3
0
1
E
3
0
2
L
3
0
3
G
3
0
4
T
3
0
5
S
3
2
9
P
3
3
0
V
4
1
9
F
4
2
2
H
4
2
3
Q
4
2
5
[1]4f0x.a . . . . . . . . . . . . . . . .
[1]4f0x.d . . . . . . . . . . . . . . . .

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
4f0x.a is apo
4f0x.d:0or
[1] 4f0x.a
-
0.1
[1] 4f0x.d -
0.1
[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
4f0x.a
4f0x.d
[1] 4f0x.a
0
0
[1] 4f0x.d 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.6 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
4f0x.a
4f0x.d
[1] 4f0x.a
0
2.3
[1] 4f0x.d 2.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.2 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
4f0x.a
4f0x.d
[1] 4f0x.a
0
3.2
[1] 4f0x.d 3.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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