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DXR_ECOLI_1_398

1-deoxy-D-xylulose 5-phosphate reductoisomerase [DXR family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DXR_ECOLI):R: Binding to substrate phosphate group (222, 227, 228)
12, 125, 150:153, 185:187, 209:214, 218, 231, 253, 254, 257, 274:276
12, 125, 150:153, 185:187, 209:214, 218, 222, 227, 228, 231, 253, 254, 257, 274:276

Full PDB list

1jvs, 1k5h, 1onn, 1ono, 1onp, 1q0h, 1q0l, 1q0q, 1t1r, 1t1s, 2egh, 3anl, 3anm, 3ann, 3r0i (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
1
2
5
D
1
5
0
S
1
5
1
E
1
5
2
G
1
8
5
S
1
8
6
H
2
0
9
N
2
1
1
W
2
1
2
M
2
1
4
I
2
1
8
S
2
2
2
N
2
2
7
K
2
2
8
E
2
3
1
S
2
5
4
H
2
5
7
P
2
7
4
M
2
7
6
[1]1jvs.b none . . . . . . . . . * . . . . . . . . *
[1]1onp.a fom,mn12 . . . . . . . . . . . . . . . . . . .
[1]1q0h.a fom11 . . . . . . . . . * . . . . . . . . *
[1]1q0l.a fom11 . . . . . . . . . . . . . . . . . . .
[1]1q0q.a dxp13 . . . . . . . . . . . . . . . . . . .
[1]1t1r.a imb20 . . . . . . . . . . . . . . . . . . .
[1]1t1s.a cbq,mg18 . . . . . . . . . . . . . . . . . . .
[1]1t1s.b cbq17 . . . . . . . . . . . . . . . . . . .
[1]2egh.b fom,mg12 . . . . . . . . . . . . . . . . . . .
[2]1onn.a none . . . . . . - - - - . . . . . . . . .
[2]1ono.a mn1 . . . . . . - - - - . . . . . . . . .
[2]3anl.a syc11 . . . . . . . . . . . . . . . . . . .
[2]3anm.b syd17 . . . . . . . . . . . . . . . . . . .
[2]3ann.a sye15 . . . . . . . . . . . . . . . . . . .
[2]3r0i.b c0k,mn21 . . . . . . - - - . . . . . . . . . .

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
S
1
2
K
1
2
5
D
1
5
0
S
1
5
1
E
1
5
2
H
1
5
3
G
1
8
5
S
1
8
6
G
1
8
7
H
2
0
9
P
2
1
0
N
2
1
1
W
2
1
2
S
2
1
3
M
2
1
4
I
2
1
8
S
2
2
2
N
2
2
7
K
2
2
8
E
2
3
1
Q
2
5
3
S
2
5
4
H
2
5
7
P
2
7
4
D
2
7
5
M
2
7
6
[1]1jvs.b . . * . . . . . . * . * * . * . . . . . . . . . . *
[1]1onp.a . . * . . . . . . . . * * . . . . . . . . . . . . .
[1]1q0h.a . . . . . . . . . * . * * . mse * . . . * . . . . . *
[1]1q0l.a . . . . . . . . . * . * * . . * . . . * . . . . . .
[1]1q0q.a . . . . . . . . . * . * * . . * . . . . . . . . . .
[1]1t1r.a . . * . . . . . . * . * * . . . . * . . . . . . . .
[1]1t1s.a . . . . . . . . . * . * * . . . . . . . . . . . . .
[1]1t1s.b . . . . . . . . . * . * * . . . . . . . . . . . . .
[1]2egh.b . . . . . . . . . . . * * . . . . . . . . . . . . .
[2]1onn.a . . . . . . . . . - - - - - - . . . . . . . . . . .
[2]1ono.a . . * . . . . . . - - - - - - . . . . . . . . . . .
[2]3anl.a . . * . . . . . . . . * . . . . . . . . . . . . . .
[2]3anm.b . . * . . . . . . . . . . . . . . . . . . . . . . .
[2]3ann.a . . . . . . . . . . . * . . . . . . . . . . . . . .
[2]3r0i.b . . * . . . . . . - - - - - . . . . . . . . . . . .

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
1jvs.b is apo
1onp.a:fom,mn
1q0h.a:fom
1q0l.a:fom
1q0q.a:dxp
1t1r.a:imb
1t1s.a:cbq,mg
1t1s.b:cbq
2egh.b:fom,mg
1onn.a is apo
1ono.a:mn
3anl.a:syc
3anm.b:syd
3ann.a:sye
3r0i.b:c0k,mn
[1] 1jvs.b
-
0.5 0 0.1 0.1 0.5 1.6 0.9 0.4 - 0.2 2.1 6.4 3.1 2.8
[1] 1onp.a -
0.5
0.1 0.3 0.6 4.4 5.1 3.9 0.4 - 0.2 1.1 3.8 4.3 3.3
[1] 1q0h.a - 0.3
0.1
0.1 0.5 4.9 5.5 4.4 0.5 - 0.1 3.5 6.5 5.6 4.9
[1] 1q0l.a - 0.4 0.2
0.2
0.3 3.3 4.9 4.1 0.4 - 0.1 3.4 6.0 5.0 4.3
[1] 1q0q.a - 0.7 0.1 0.2
0.1
3.4 6.0 5.3 0.7 - 0.3 3.7 5.9 5.3 5.2
[1] 1t1r.a - 0.9 0.6 0.5 0.8
0.1
1.0 0.4 0.8 - 0.1 3.6 5.8 4.3 3.8
[1] 1t1s.a - 0.3 0.2 0.3 0.3 0
0.2
0.1 0.5 - 0.1 3.2 5.6 4.0 3.8
[1] 1t1s.b - 0.9 0.4 0.6 0.7 0.4 0.5
0.1
0.8 - 0.2 3.6 5.9 4.5 4.6
[1] 2egh.b - 0.3 0.1 0.2 0.3 2.8 5.2 4.6
0.4
- 0.2 2.5 2.5 3.9 3.7
[2] 1onn.a - 0.7 0.3 0.6 0.4 0.6 0.8 0.3 0.4
-
0.2 0.3 0.3 0.4 0.7
[2] 1ono.a - 0.6 0.2 0.2 0.5 0.6 1.8 0.8 0.3 -
0.3
0.1 0.1 0.1 0.4
[2] 3anl.a - 0.8 0 0.2 0.2 1.2 2.0 1.3 0.6 - 0.3
0.1
1.7 0.3 1.4
[2] 3anm.b - 0.7 0.1 0.1 0.2 0.8 2.2 1.3 0.3 - 0.3 0
0
0 0.5
[2] 3ann.a - 0.5 0 0.2 0.1 0.8 1.7 1.1 0.7 - 0.2 0 1.3
0
1.3
[2] 3r0i.b - 0.7 0.2 0.2 0.1 0.8 1.7 1.3 0.4 - 0.3 0.1 0.1 0
0.5
[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
1jvs.b
1onp.a
1q0h.a
1q0l.a
1q0q.a
1t1r.a
1t1s.a
1t1s.b
2egh.b
1onn.a
1ono.a
3anl.a
3anm.b
3ann.a
3r0i.b
[1] 1jvs.b
0
.17 .24 .18 .15 .12 .13 .11 .12 .32 .30 .21 .30 .24 .30
[1] 1onp.a .17
0
.29 .22 .20 .16 .18 .17 .07 .26 .25 .20 .28 .20 .25
[1] 1q0h.a .24 .29
0
.11 .14 .25 .24 .26 .28 .49 .49 .37 .49 .39 .48
[1] 1q0l.a .18 .22 .11
0
.09 .17 .15 .17 .21 .39 .39 .30 .39 .31 .39
[1] 1q0q.a .15 .20 .14 .09
0
.17 .20 .20 .17 .41 .41 .29 .39 .30 .40
[1] 1t1r.a .12 .16 .25 .17 .17
0
.07 .07 .14 .27 .29 .20 .29 .19 .27
[1] 1t1s.a .13 .18 .24 .15 .20 .07
0
.07 .17 .29 .31 .23 .32 .23 .31
[1] 1t1s.b .11 .17 .26 .17 .20 .07 .07
0
.14 .26 .31 .22 .32 .23 .30
[1] 2egh.b .12 .07 .28 .21 .17 .14 .17 .14
0
.26 .26 .17 .26 .19 .24
[2] 1onn.a .32 .26 .49 .39 .41 .27 .29 .26 .26
0
.05 .16 .07 .14 .05
[2] 1ono.a .30 .25 .49 .39 .41 .29 .31 .31 .26 .05
0
.13 .04 .13 .02
[2] 3anl.a .21 .20 .37 .30 .29 .20 .23 .22 .17 .16 .13
0
.13 .05 .14
[2] 3anm.b .30 .28 .49 .39 .39 .29 .32 .32 .26 .07 .04 .13
0
.14 .04
[2] 3ann.a .24 .20 .39 .31 .30 .19 .23 .23 .19 .14 .13 .05 .14
0
.11
[2] 3r0i.b .30 .25 .48 .39 .40 .27 .31 .30 .24 .05 .02 .14 .04 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 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
1jvs.b
1onp.a
1q0h.a
1q0l.a
1q0q.a
1t1r.a
1t1s.a
1t1s.b
2egh.b
1onn.a
1ono.a
3anl.a
3anm.b
3ann.a
3r0i.b
[1] 1jvs.b
0
1.5 1.6 1.6 1.6 0.4 0.5 0.6 1.5 0.6 0.4 0.8 0.9 0.8 0.5
[1] 1onp.a 1.5
0
1.7 1.7 1.7 1.4 1.4 1.5 1.4 0.5 0.4 1.6 1.7 1.7 0.6
[1] 1q0h.a 1.6 1.7
0
0.2 0.6 1.4 1.4 1.4 0.9 1.3 1.1 1.5 1.8 1.7 1.3
[1] 1q0l.a 1.6 1.7 0.2
0
0.6 1.5 1.4 1.5 1.0 1.4 1.1 1.5 1.8 1.8 1.3
[1] 1q0q.a 1.6 1.7 0.6 0.6
0
1.4 1.4 1.5 1.0 1.2 1.0 1.6 1.9 1.8 1.2
[1] 1t1r.a 0.4 1.4 1.4 1.5 1.4
0
0.2 0.5 1.3 0.5 0.4 0.8 1.0 0.8 0.4
[1] 1t1s.a 0.5 1.4 1.4 1.4 1.4 0.2
0
0.5 1.3 0.5 0.4 0.8 1.0 0.9 0.4
[1] 1t1s.b 0.6 1.5 1.4 1.5 1.5 0.5 0.5
0
1.4 0.5 0.6 0.9 1.1 1.0 0.6
[1] 2egh.b 1.5 1.4 0.9 1.0 1.0 1.3 1.3 1.4
0
0.7 0.4 1.3 1.7 1.6 0.6
[2] 1onn.a 0.6 0.5 1.3 1.4 1.2 0.5 0.5 0.5 0.7
0
0.5 0.6 0.7 0.6 0.4
[2] 1ono.a 0.4 0.4 1.1 1.1 1.0 0.4 0.4 0.6 0.4 0.5
0
0.5 0.5 0.5 0.3
[2] 3anl.a 0.8 1.6 1.5 1.5 1.6 0.8 0.8 0.9 1.3 0.6 0.5
0
0.6 0.4 0.5
[2] 3anm.b 0.9 1.7 1.8 1.8 1.9 1.0 1.0 1.1 1.7 0.7 0.5 0.6
0
0.5 0.6
[2] 3ann.a 0.8 1.7 1.7 1.8 1.8 0.8 0.9 1.0 1.6 0.6 0.5 0.4 0.5
0
0.5
[2] 3r0i.b 0.5 0.6 1.3 1.3 1.2 0.4 0.4 0.6 0.6 0.4 0.3 0.5 0.6 0.5
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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1jvs.b
1onp.a
1q0h.a
1q0l.a
1q0q.a
1t1r.a
1t1s.a
1t1s.b
2egh.b
1onn.a
1ono.a
3anl.a
3anm.b
3ann.a
3r0i.b
[1] 1jvs.b
0
2.5 2.0 2.0 2.0 1.1 1.1 1.2 2.0 0.9 0.8 1.9 1.5 1.9 0.9
[1] 1onp.a 2.5
0
2.5 2.5 2.6 2.5 2.5 2.5 2.3 0.8 0.7 2.4 2.4 2.5 1.0
[1] 1q0h.a 2.0 2.5
0
0.6 1.2 1.8 1.8 1.9 1.7 1.6 1.5 1.9 2.1 2.1 1.7
[1] 1q0l.a 2.0 2.5 0.6
0
1.1 1.7 1.7 1.8 1.6 1.6 1.5 2.0 2.1 2.1 1.6
[1] 1q0q.a 2.0 2.6 1.2 1.1
0
1.9 1.9 2.0 1.7 1.6 1.4 2.2 2.3 2.4 1.8
[1] 1t1r.a 1.1 2.5 1.8 1.7 1.9
0
0.5 0.9 1.9 1.0 1.0 1.5 1.6 1.5 1.2
[1] 1t1s.a 1.1 2.5 1.8 1.7 1.9 0.5
0
0.9 1.9 1.0 1.0 1.5 1.6 1.6 1.2
[1] 1t1s.b 1.2 2.5 1.9 1.8 2.0 0.9 0.9
0
1.9 0.9 1.1 1.6 1.6 1.6 1.3
[1] 2egh.b 2.0 2.3 1.7 1.6 1.7 1.9 1.9 1.9
0
1.1 0.9 2.2 2.3 2.4 1.1
[2] 1onn.a 0.9 0.8 1.6 1.6 1.6 1.0 1.0 0.9 1.1
0
0.7 1.1 1.1 1.1 0.8
[2] 1ono.a 0.8 0.7 1.5 1.5 1.4 1.0 1.0 1.1 0.9 0.7
0
1.0 0.9 1.0 0.6
[2] 3anl.a 1.9 2.4 1.9 2.0 2.2 1.5 1.5 1.6 2.2 1.1 1.0
0
1.6 0.4 1.2
[2] 3anm.b 1.5 2.4 2.1 2.1 2.3 1.6 1.6 1.6 2.3 1.1 0.9 1.6
0
1.5 1.0
[2] 3ann.a 1.9 2.5 2.1 2.1 2.4 1.5 1.6 1.6 2.4 1.1 1.0 0.4 1.5
0
1.2
[2] 3r0i.b 0.9 1.0 1.7 1.6 1.8 1.2 1.2 1.3 1.1 0.8 0.6 1.2 1.0 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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