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ALKB5_HUMAN_68_293

RNA demethylase ALKBH5 [AlkB family]

Composition of the binding site

Protein chains monomer
A1 (ALKB5_HUMAN):130, 200:202, 233, 234130, 200:202, 233, 234
Metals (Me):Mn

Full PDB list

4nj4, 4nrm, 4nro, 4nrp, 4nrq, 4o61, 4o7x, 4oct (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
R
1
3
0
C
2
0
0
I
2
0
1
V
2
0
2
Q
2
3
3
[1]4nj4.a un918 . * . . . Mn
[1]4oct.a none . . . . . Mn

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
R
1
3
0
C
2
0
0
I
2
0
1
V
2
0
2
Q
2
3
3
F
2
3
4
[1]4nj4.a . * . . . . Mn
[1]4oct.a . . . * . . Mn

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
4nj4.a:un9
4oct.a is apo
[1] 4nj4.a
0.4
-
[1] 4oct.a 0.8
-
[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
4nj4.a
4oct.a
[1] 4nj4.a
0
.17
[1] 4oct.a .17
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
4nj4.a
4oct.a
[1] 4nj4.a
0
0.8
[1] 4oct.a 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
4nj4.a
4oct.a
[1] 4nj4.a
0
1.4
[1] 4oct.a 1.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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