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DPRE1_MYCTU_2_461

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DPRE1_MYCTU):D: FAD-binding PCMH-type (60, 117, 132:134)
228, 230, 314:325, 328, 334, 336, 363:365, 367, 369, 385:387, 389, 418
60, 117, 132:134, 228, 230, 314:325, 328, 334, 336, 363:365, 367, 369, 385:387, 389, 418
Cofactors (cF):fad

Full PDB list

4fdn, 4fdo, 4fdp, 4feh, 4ff6, 4kw5, 4ncr, 4p8c, 4p8h, 4p8k, 4p8l, 4p8m, 4p8n, 4p8p, 4p8t, 4p8y, 4pfa, 4pfd (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
Y
6
0
G
1
1
7
H
1
3
2
G
1
3
3
K
1
3
4
S
2
2
8
W
2
3
0
Y
3
1
4
L
3
1
7
F
3
2
0
G
3
2
1
N
3
2
4
R
3
2
5
Q
3
3
4
Q
3
3
6
L
3
6
3
N
3
6
4
V
3
6
5
K
3
6
7
N
3
8
5
I
3
8
6
C
3
8
7
K
4
1
8
[1]4fdn.a 0t423 . . . . . . . . - - - . . . . . . . . . . * . fad
[1]4kw5.a 1w625 . . . . . . . . - - - - - . . . . . . . . . . fad
[1]4ncr.b 26j30 . . . . . . . . - - - - - . . . . . . . . * . fad
[1]4p8h.a o9528 . . . . . . . . - - - - - . . . . . . . . * . fad
[1]4p8m.a r5828 . . . . . . . . . - - - - . . . . . . . . . . fad
[1]4p8y.a 38c27 . . . . . . . . . . . . . . . . . . . . . . . fad
[1]4pfa.b n7726 . . . . . . . . - - - - - . . . . . . . . * . fad
[1]4pfd.a 2r229 . . . . . . . . . - - - - . . . . . . . . . . fad
[2]4feh.a none . . . . . . . . - - - . . . . . . . . . . . . fad
[2]4p8c.a y2229 . . . . . . . . . . . - - . . . . . . . . . . fad
[2]4p8l.a 36c26 . . . . . . . . . . . . . . . . . . . . . . . fad
[2]4p8n.a r5728 . . . . . . . . . . . . . . . . . . . . . . . fad
[2]4p8p.a rg226 . . . . . . . . . . . - - . . . . . . . . . . fad
[2]4p8t.a r2627 . . . . . . . . . . . . . . . . . . . . . . . fad
[3]4fdo.a 0t524 . . . . . . . . . . . . . . . . . . . . . . . fad

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 cF
Y
6
0
G
1
1
7
H
1
3
2
G
1
3
3
K
1
3
4
S
2
2
8
W
2
3
0
Y
3
1
4
H
3
1
5
P
3
1
6
L
3
1
7
D
3
1
8
M
3
1
9
F
3
2
0
G
3
2
1
E
3
2
2
W
3
2
3
N
3
2
4
R
3
2
5
G
3
2
8
Q
3
3
4
Q
3
3
6
L
3
6
3
N
3
6
4
V
3
6
5
K
3
6
7
F
3
6
9
N
3
8
5
I
3
8
6
C
3
8
7
D
3
8
9
K
4
1
8
[1]4fdn.a . . . . . . * . - - - - - - - - . . . . . . . . . . . . . * . . fad
[1]4kw5.a . . . . . . * . . . - - - - - - - - - - . . . . . . . . . . . . fad
[1]4ncr.b . . . . . . * . - - - - - - - - - - - - . . . . . . . . . * . . fad
[1]4p8h.a . . . . . . * . - - - - - - - - - - - - . . . . . . . . . * . . fad
[1]4p8m.a . . . . . . * . . . . - - - - - - - - . . . . . . . . . . . . . fad
[1]4p8y.a . . . . . . * . . . * . . . . . . * . - . . . . . . . . . * . . fad
[1]4pfa.b . . . . . . * . . . - - - - - - - - - - . . . . . . . . . * . . fad
[1]4pfd.a . . . . . . * . . * * . . - - - - - - . . . . . . . . . . . . . fad
[2]4feh.a . . . . . . . . * - - - - - - - . . . . . . . . . . . . . . . . fad
[2]4p8c.a . . . . . . . . . . * . . . . . . - - . . . . . . . . . . * . . fad
[2]4p8l.a . . . . . . . . . . * . . . . . . * . . . . . . . . . . . * . . fad
[2]4p8n.a . . . . . . . . . . * . . . . . . * * - . . . . . . . . . * . . fad
[2]4p8p.a . . . . . . . . . . * . . . . . . - - - . . . . . . . . . * . . fad
[2]4p8t.a . . . . . . . . . . * . . . . . . . * . . . . . . . . . . . . . fad
[3]4fdo.a . . . . . . * . . * * . . * * . . . . . . . . . . . . . . . . . fad

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
4fdn.a:0t4
4kw5.a:1w6
4ncr.b:26j
4p8h.a:o95
4p8m.a:r58
4p8y.a:38c
4pfa.b:n77
4pfd.a:2r2
4feh.a is apo
4p8c.a:y22
4p8l.a:36c
4p8n.a:r57
4p8p.a:rg2
4p8t.a:r26
4fdo.a:0t5
[1] 4fdn.a
0.4
0 0.3 0.8 0 0.1 0.7 0.1 - 3.3 0.1 0.1 2.8 1.9 0.6
[1] 4kw5.a 0.2
0
0.2 0.9 0 0.2 0.5 1.0 - 3.7 0.2 0.2 3.2 2.0 0.3
[1] 4ncr.b 0.7 0.6
0.4
0.9 0.2 0.3 0.7 1.3 - 2.9 0.2 0.2 2.1 1.5 0.8
[1] 4p8h.a 0.4 0.2 0.3
0.8
0.4 0.4 0.4 0.5 - 3.5 0.4 0.4 2.5 1.6 0.7
[1] 4p8m.a 0.1 0.1 0 1.3
0
0 0.3 1.1 - 3.3 0 0 2.9 2.3 0.5
[1] 4p8y.a 0.7 0.5 1.4 2.2 1.0
0
0.9 1.0 - 4.1 0 0 3.7 2.3 0.8
[1] 4pfa.b 0.7 0.2 0.3 1.1 0 0
0.6
0.9 - 3.5 0 0 3.0 1.8 0.7
[1] 4pfd.a 0.2 2.3 0.6 4.8 0.4 0.8 1.2
0
- 4.3 0.5 1.3 3.8 2.9 0.3
[2] 4feh.a 0.1 0 0 3.6 0.1 0.2 1.5 0
-
0.2 0.1 0.1 0.2 0.1 0.1
[2] 4p8c.a 0.9 0.1 1.1 4.2 1.4 1.4 3.5 0.6 -
0
1.6 1.2 0 0 0.9
[2] 4p8l.a 0.5 1.1 1.8 3.3 1.5 0.2 1.6 1.6 - 0.2
0
0 0 0.1 0.9
[2] 4p8n.a 0.8 0.8 1.6 3.3 1.8 0.1 2.1 1.5 - 0 0.1
0.1
0 0.3 0.8
[2] 4p8p.a 1.0 0.1 0.7 4.4 1.1 0.5 3.0 0.6 - 0 0.5 0.3
0
0 0.9
[2] 4p8t.a 0.7 0.9 2.2 4.3 1.4 2.4 3.0 1.6 - 0 2.4 2.3 0
0
0.9
[3] 4fdo.a 0.2 3.1 4.8 6.2 4.9 4.2 6.0 2.1 - 5.5 4.0 5.5 4.7 3.7
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
4fdn.a
4kw5.a
4ncr.b
4p8h.a
4p8m.a
4p8y.a
4pfa.b
4pfd.a
4feh.a
4p8c.a
4p8l.a
4p8n.a
4p8p.a
4p8t.a
4fdo.a
[1] 4fdn.a
0
.05 .06 .02 .06 .11 .05 .15 .19 .21 .25 .26 .21 .27 .34
[1] 4kw5.a .05
0
.10 .06 .03 .14 .04 .16 .24 .25 .29 .31 .25 .31 .37
[1] 4ncr.b .06 .10
0
.05 .11 .16 .08 .20 .22 .23 .27 .28 .23 .29 .39
[1] 4p8h.a .02 .06 .05
0
.07 .13 .05 .16 .21 .23 .27 .28 .23 .29 .35
[1] 4p8m.a .06 .03 .11 .07
0
.15 .06 .17 .25 .25 .30 .31 .25 .32 .37
[1] 4p8y.a .11 .14 .16 .13 .15
0
.14 .16 .30 .25 .18 .20 .25 .27 .37
[1] 4pfa.b .05 .04 .08 .05 .06 .14
0
.17 .24 .24 .29 .31 .24 .30 .38
[1] 4pfd.a .15 .16 .20 .16 .17 .16 .17
0
.34 .18 .25 .26 .19 .25 .22
[2] 4feh.a .19 .24 .22 .21 .25 .30 .24 .34
0
.22 .25 .27 .22 .26 .52
[2] 4p8c.a .21 .25 .23 .23 .25 .25 .24 .18 .22
0
.12 .12 .01 .07 .35
[2] 4p8l.a .25 .29 .27 .27 .30 .18 .29 .25 .25 .12
0
.02 .12 .12 .45
[2] 4p8n.a .26 .31 .28 .28 .31 .20 .31 .26 .27 .12 .02
0
.12 .11 .45
[2] 4p8p.a .21 .25 .23 .23 .25 .25 .24 .19 .22 .01 .12 .12
0
.06 .35
[2] 4p8t.a .27 .31 .29 .29 .32 .27 .30 .25 .26 .07 .12 .11 .06
0
.40
[3] 4fdo.a .34 .37 .39 .35 .37 .37 .38 .22 .52 .35 .45 .45 .35 .40
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
4fdn.a
4kw5.a
4ncr.b
4p8h.a
4p8m.a
4p8y.a
4pfa.b
4pfd.a
4feh.a
4p8c.a
4p8l.a
4p8n.a
4p8p.a
4p8t.a
4fdo.a
[1] 4fdn.a
0
0.5 1.4 0.4 2.3 3.2 0.6 2.4 0.4 2.4 3.3 3.2 1.7 3.3 0.4
[1] 4kw5.a 0.5
0
1.4 0.6 0.4 1.0 0.4 1.5 1.2 0.9 1.0 1.0 1.0 1.0 1.6
[1] 4ncr.b 1.4 1.4
0
1.2 1.4 1.5 1.3 1.4 1.5 1.5 1.5 1.5 1.5 1.5 1.5
[1] 4p8h.a 0.4 0.6 1.2
0
0.6 0.7 0.6 0.4 0.5 0.7 0.7 0.7 0.7 0.7 0.5
[1] 4p8m.a 2.3 0.4 1.4 0.6
0
3.3 0.5 2.2 2.5 2.8 3.7 3.2 1.7 2.9 3.1
[1] 4p8y.a 3.2 1.0 1.5 0.7 3.3
0
1.2 3.6 3.2 0.8 0.3 0.2 0.5 0.9 4.1
[1] 4pfa.b 0.6 0.4 1.3 0.6 0.5 1.2
0
1.6 1.3 1.1 1.2 1.1 1.1 1.1 1.8
[1] 4pfd.a 2.4 1.5 1.4 0.4 2.2 3.6 1.6
0
2.3 3.2 4.0 3.6 1.8 3.3 2.3
[2] 4feh.a 0.4 1.2 1.5 0.5 2.5 3.2 1.3 2.3
0
2.6 3.4 3.3 1.8 3.4 0.4
[2] 4p8c.a 2.4 0.9 1.5 0.7 2.8 0.8 1.1 3.2 2.6
0
1.6 0.7 0.2 0.8 3.9
[2] 4p8l.a 3.3 1.0 1.5 0.7 3.7 0.3 1.2 4.0 3.4 1.6
0
0.2 0.5 1.4 4.2
[2] 4p8n.a 3.2 1.0 1.5 0.7 3.2 0.2 1.1 3.6 3.3 0.7 0.2
0
0.4 0.8 4.1
[2] 4p8p.a 1.7 1.0 1.5 0.7 1.7 0.5 1.1 1.8 1.8 0.2 0.5 0.4
0
0.4 3.5
[2] 4p8t.a 3.3 1.0 1.5 0.7 2.9 0.9 1.1 3.3 3.4 0.8 1.4 0.8 0.4
0
4.2
[3] 4fdo.a 0.4 1.6 1.5 0.5 3.1 4.1 1.8 2.3 0.4 3.9 4.2 4.1 3.5 4.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.3 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
4fdn.a
4kw5.a
4ncr.b
4p8h.a
4p8m.a
4p8y.a
4pfa.b
4pfd.a
4feh.a
4p8c.a
4p8l.a
4p8n.a
4p8p.a
4p8t.a
4fdo.a
[1] 4fdn.a
0
1.0 1.9 1.0 1.9 3.5 1.2 2.1 0.5 2.6 3.8 3.7 2.2 3.8 0.8
[1] 4kw5.a 1.0
0
1.8 1.2 0.7 1.0 0.9 2.4 2.1 1.9 1.9 1.8 1.8 1.8 2.6
[1] 4ncr.b 1.9 1.8
0
1.8 1.7 1.9 1.8 1.7 2.0 2.4 2.4 2.4 2.4 2.4 2.1
[1] 4p8h.a 1.0 1.2 1.8
0
1.1 1.2 1.3 1.0 1.0 2.0 2.0 2.0 2.0 2.0 1.2
[1] 4p8m.a 1.9 0.7 1.7 1.1
0
3.1 0.9 2.9 2.6 3.0 3.6 3.3 2.5 3.0 3.5
[1] 4p8y.a 3.5 1.0 1.9 1.2 3.1
0
1.3 3.5 3.8 1.8 1.5 1.5 1.6 1.9 4.8
[1] 4pfa.b 1.2 0.9 1.8 1.3 0.9 1.3
0
2.5 2.2 1.9 1.9 1.9 1.8 1.9 2.7
[1] 4pfd.a 2.1 2.4 1.7 1.0 2.9 3.5 2.5
0
2.3 3.5 3.9 3.8 2.8 3.6 2.3
[2] 4feh.a 0.5 2.1 2.0 1.0 2.6 3.8 2.2 2.3
0
2.7 3.9 3.8 2.3 3.9 0.8
[2] 4p8c.a 2.6 1.9 2.4 2.0 3.0 1.8 1.9 3.5 2.7
0
1.3 1.0 0.6 0.9 4.5
[2] 4p8l.a 3.8 1.9 2.4 2.0 3.6 1.5 1.9 3.9 3.9 1.3
0
0.7 0.7 1.5 4.9
[2] 4p8n.a 3.7 1.8 2.4 2.0 3.3 1.5 1.9 3.8 3.8 1.0 0.7
0
0.8 1.2 5.0
[2] 4p8p.a 2.2 1.8 2.4 2.0 2.5 1.6 1.8 2.8 2.3 0.6 0.7 0.8
0
0.8 4.2
[2] 4p8t.a 3.8 1.8 2.4 2.0 3.0 1.9 1.9 3.6 3.9 0.9 1.5 1.2 0.8
0
4.9
[3] 4fdo.a 0.8 2.6 2.1 1.2 3.5 4.8 2.7 2.3 0.8 4.5 4.9 5.0 4.2 4.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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