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DGOA_ECOLI_1_205

2-dehydro-3-deoxy-6-phosphogalactonate aldolase [KHG/KDPG aldolase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DGOA_ECOLI):R: Substrate binding (176, 177)
12, 14, 66, 85:87, 126, 128, 154:156
12, 14, 66, 85:87, 126, 128, 154:156, 176, 177

Full PDB list

2v81, 2v82

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
2
R
1
4
T
6
6
V
8
5
T
8
6
P
8
7
K
1
2
6
F
1
2
8
V
1
5
4
G
1
5
5
G
1
7
6
S
1
7
7
[1]2v81.a none . . . . . . . . . . . .
[1]2v82.a kdp15 . . . . . . * . . . . .

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
I
1
2
R
1
4
T
6
6
V
8
5
T
8
6
P
8
7
K
1
2
6
F
1
2
8
V
1
5
4
G
1
5
5
G
1
5
6
G
1
7
6
S
1
7
7
[1]2v81.a . . . . . . . . . . . . .
[1]2v82.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
2v81.a is apo
2v82.a:kdp
[1] 2v81.a
-
0.3
[1] 2v82.a -
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
2v81.a
2v82.a
[1] 2v81.a
0
.02
[1] 2v82.a .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
2v81.a
2v82.a
[1] 2v81.a
0
0.3
[1] 2v82.a 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
2v81.a
2v82.a
[1] 2v81.a
0
1.1
[1] 2v82.a 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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