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DPRE1_MYCS2_58_460

Decaprenylphosphoryl-beta-D-ribose oxidase [DprE1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DPRE1_MYCS2):D: FAD-binding PCMH-type (116, 131:133)
315:321, 362, 364, 366, 384, 386, 417
116, 131:133, 315:321, 362, 364, 366, 384, 386, 417

Full PDB list

4aut, 4f4q, 4g3t, 4g3u (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
G
1
1
6
H
1
3
1
G
1
3
2
K
1
3
3
L
3
6
2
V
3
6
4
K
3
6
6
N
3
8
4
C
3
8
6
K
4
1
7
[1]4f4q.a 0sk28 . . . . . . . . * .
[2]4aut.a none . . . . . . . . . .

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
G
1
1
6
H
1
3
1
G
1
3
2
K
1
3
3
P
3
1
5
L
3
1
6
D
3
1
7
M
3
1
8
F
3
1
9
G
3
2
0
E
3
2
1
L
3
6
2
V
3
6
4
K
3
6
6
N
3
8
4
C
3
8
6
K
4
1
7
[1]4f4q.a . . . . . - - - - - - . . . . * .
[2]4aut.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
4f4q.a:0sk
4aut.a is apo
[1] 4f4q.a
0.4
-
[2] 4aut.a 9.4
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
4f4q.a
4aut.a
[1] 4f4q.a
0
.58
[2] 4aut.a .58
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
4f4q.a
4aut.a
[1] 4f4q.a
0
1.7
[2] 4aut.a 1.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
4f4q.a
4aut.a
[1] 4f4q.a
0
2.0
[2] 4aut.a 2.0
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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