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DNRD_STRGJ_1_144

Aklanonic acid methyl ester cyclase AcmA [Polyketide cyclase DnrD family]

Composition of the binding site

Protein chains homodimer
A1 (DNRD_STRGJ):33, 36, 39, 50, 51, 54, 55, 59, 83, 91, 92, 94, 105, 121, 123, 125, 128, 12933, 36, 39, 50, 51, 54, 55, 59, 83, 91, 92, 94, 105, 121, 123, 125, 128, 129
A2 (DNRD_STRGJ):122122

Full PDB list

2f98, 2f99

Pocket contact map

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PDB.ch
   
ligand
A1 A2
N
3
3
T
3
6
F
3
9
I
5
0
N
5
1
W
5
4
V
5
5
F
5
9
M
9
1
V
9
2
M
9
4
D
1
2
1
P
1
2
3
Y
1
2
5
T
1
2
8
W
1
2
2
[1]2f98.b ngv28 . . . . . . . . . . . . . . . .
[1]2f99.d akv30 . . . . . . . . . . . . . . . .

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 A2
N
3
3
T
3
6
F
3
9
I
5
0
N
5
1
W
5
4
V
5
5
F
5
9
L
8
3
M
9
1
V
9
2
M
9
4
Q
1
0
5
D
1
2
1
P
1
2
3
Y
1
2
5
T
1
2
8
Y
1
2
9
W
1
2
2
[1]2f98.b . . . . . . . . . . . . . . . . . . .
[1]2f99.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
2f98.b:ngv
2f99.d:akv
[1] 2f98.b
0
0.1
[1] 2f99.d 1.3
0
[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
2f98.b
2f99.d
[1] 2f98.b
0
.07
[1] 2f99.d .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
2f98.b
2f99.d
[1] 2f98.b
0
0.2
[1] 2f99.d 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
2f98.b
2f99.d
[1] 2f98.b
0
0.7
[1] 2f99.d 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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