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ASQJ_EMENI_109_416

Iron/alpha-ketoglutarate-dependent dioxygenase asqJ [PhyH family]

Composition of the binding site

Protein chains monomer
A1 (ASQJ_EMENI):178, 180, 181, 187, 226, 230, 239, 240, 242, 244, 245, 247, 335178, 180, 181, 187, 226, 230, 239, 240, 242, 244, 245, 247, 335
Metals (Me):Ni

Full PDB list

5dap, 5daq, 5dav, 5daw, 5dax

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
N
1
7
8
V
1
8
0
L
1
8
1
L
1
8
7
M
2
2
6
M
2
3
0
Q
2
3
9
P
2
4
0
H
2
4
2
D
2
4
4
M
2
4
5
F
2
4
7
T
3
3
5
[1]5dap.a none . . . . . . . . . . . . . Ni
[1]5daq.a 58d23 . . . . . . . . . . . . . Ni
[1]5dav.a 58j23 . . . . . . . . . . . . . Ni
[1]5daw.a 58k21 . . . . . . . . . . . . . Ni
[1]5dax.a 58l20 . . . . . . . . . . . . . Ni

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
N
1
7
8
V
1
8
0
L
1
8
1
L
1
8
7
M
2
2
6
M
2
3
0
Q
2
3
9
P
2
4
0
H
2
4
2
D
2
4
4
M
2
4
5
F
2
4
7
T
3
3
5
[1]5dap.a . . . . . . . . . . . . . Ni
[1]5daq.a . . . . . . . . . . . . . Ni
[1]5dav.a . . . . . . . . . . . . . Ni
[1]5daw.a . . . . . . . . . . . . . Ni
[1]5dax.a . . . . . . . . . . . . . Ni

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
5dap.a is apo
5daq.a:58d
5dav.a:58j
5daw.a:58k
5dax.a:58l
[1] 5dap.a
-
0 0 0 0
[1] 5daq.a -
0
0 0 0.1
[1] 5dav.a - 0
0
0 0
[1] 5daw.a - 0 0
0
0
[1] 5dax.a - 0 0 0
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
5dap.a
5daq.a
5dav.a
5daw.a
5dax.a
[1] 5dap.a
0
.01 0 0 0
[1] 5daq.a .01
0
.01 .01 .01
[1] 5dav.a 0 .01
0
0 0
[1] 5daw.a 0 .01 0
0
0
[1] 5dax.a 0 .01 0 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
5dap.a
5daq.a
5dav.a
5daw.a
5dax.a
[1] 5dap.a
0
0.2 0.2 0.2 0.2
[1] 5daq.a 0.2
0
0.2 0.1 0.2
[1] 5dav.a 0.2 0.2
0
0.2 0.2
[1] 5daw.a 0.2 0.1 0.2
0
0.1
[1] 5dax.a 0.2 0.2 0.2 0.1
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
5dap.a
5daq.a
5dav.a
5daw.a
5dax.a
[1] 5dap.a
0
0.3 0.5 0.2 0.2
[1] 5daq.a 0.3
0
0.6 0.1 0.2
[1] 5dav.a 0.5 0.6
0
0.6 0.6
[1] 5daw.a 0.2 0.1 0.6
0
0.1
[1] 5dax.a 0.2 0.2 0.6 0.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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