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DXR_PLAF7_75_488

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DXR_PLAF7):R: Binding to substrate phosphate group (269, 270)
R: Substrate binding (311, 312, 315)
205, 231:233, 271, 272, 293:298, 302, 303, 306, 338, 341, 358:360, 363
205, 231:233, 269:272, 293:298, 302, 303, 306, 311, 312, 315, 338, 341, 358:360, 363
Metals (Me):Mg/Mn

Full PDB list

3au8, 3au9, 3aua, 3wqq, 3wqr, 3wqs, 4gae, 4kp7, 4y67, 4y6p, 4y6r, 4y6s, 5jaz, 5jbi, 5jc1, 5jmp, 5jmw, 5jnl, 5jo0

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
K
2
0
5
D
2
3
1
S
2
3
2
E
2
3
3
S
2
6
9
S
2
7
0
H
2
9
3
P
2
9
4
K
2
9
5
W
2
9
6
M
2
9
8
I
3
0
2
T
3
0
3
S
3
0
6
N
3
1
1
K
3
1
2
E
3
1
5
C
3
3
8
H
3
4
1
P
3
5
8
D
3
5
9
M
3
6
0
P
3
6
3
[1]3au8.a none . . . . . . - - - - - . . . . . . . . . . . . Mn
[1]3wqq.a ib319 . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3wqr.a lsx20 . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3wqs.b kbk20 . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4gae.b fob,foq36 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]4kp7.a 1uq18 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]4y67.a rc521 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]4y6p.a r7722 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]5jaz.a lc525 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]5jbi.a 6j823 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]5jc1.a 6jb23 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]5jmp.a lc722 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]5jmw.a l5022 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]5jnl.a l5425 . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]5jo0.a l5622 . . . . . . . . . . . . . . . . . . . . . . . Mn
[2]3au9.a fom11 . . . . . . . . . . . . . . . . . . . . . . . Mg
[2]3aua.b f9812 . . . . . . . . . . . . . . . . . . . . . . . Mg
[2]4y6r.a rf718 . . . . . . . . . . . . . . . . . . . . . . . Mn
[2]4y6s.a 48s19 . . . . . . . . . . . . . . . . . . . . . . . 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
K
2
0
5
D
2
3
1
S
2
3
2
E
2
3
3
S
2
6
9
S
2
7
0
G
2
7
1
G
2
7
2
H
2
9
3
P
2
9
4
K
2
9
5
W
2
9
6
K
2
9
7
M
2
9
8
I
3
0
2
T
3
0
3
S
3
0
6
N
3
1
1
K
3
1
2
E
3
1
5
C
3
3
8
H
3
4
1
P
3
5
8
D
3
5
9
M
3
6
0
P
3
6
3
[1]3au8.a . . . . . . . . - - - - - - . . . . . . . . . . . . Mn
[1]3wqq.a . . . . . . . . . . . * . * . . . . . . . . . . . . Mg
[1]3wqr.a . . . . . . . . . . . * . . . . . . . . . . . . . . Mg
[1]3wqs.b . . . . . . . . . . . * . * . . . . . . . . . . . . Mg
[1]4gae.b . . . . . . . . . . . * . * . . . . . . . . . . . . Mn
[1]4kp7.a . . . . . . . . . . * * . * . . . . . . . . . . . . Mn
[1]4y67.a . . . . . . . . . . * * . * . . . . . . . . . . . . Mn
[1]4y6p.a . . . . . . . . . . * * . * . . . . . . . . . . . . Mn
[1]5jaz.a . . . . . . . . . . . * . * . . . . . . . . . . . . Mn
[1]5jbi.a . . . . . . . . . . * * . * . . . . . . . . . . . . Mn
[1]5jc1.a . . . . . . . . . . . * . * . . . . . . . . . . . . Mn
[1]5jmp.a . . . . . . . . . . * * . * . . . . . . . . . . . . Mn
[1]5jmw.a . . . . . . . . . . . * . * . . . . . . . . . . . . Mn
[1]5jnl.a . . . . . . . . . . * * . * . . . . . . . . . . . . Mn
[1]5jo0.a . . . . . . . . . . . * . * . . . . . . . . . . . . Mn
[2]3au9.a . . . . . . . . * . * * . * . . . . . . . . . . . . Mg
[2]3aua.b . . . . . . . . * . * * . * . . . . . . . . . . . . Mg
[2]4y6r.a . . . . . . . . . . * * . . . . . . . . . . . . . . Mn
[2]4y6s.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3au8.a is apo
3wqq.a:ib3
3wqr.a:lsx
3wqs.b:kbk
4gae.b:fob,foq
4kp7.a:1uq
4y67.a:rc5
4y6p.a:r77
5jaz.a:lc5
5jbi.a:6j8
5jc1.a:6jb
5jmp.a:lc7
5jmw.a:l50
5jnl.a:l54
5jo0.a:l56
3au9.a:fom
3aua.b:f98
4y6r.a:rf7
4y6s.a:48s
[1] 3au8.a
-
0.2 0.3 0.3 0.1 0.4 0.2 0.2 0.1 0.2 0.1 0.1 0.3 0.6 0.1 0.5 0.3 0.2 0.2
[1] 3wqq.a -
0.1
0.1 0.5 0.1 0.2 0.1 0.3 0.1 0.4 0.1 0.2 0.3 0.9 0.1 0.3 0.2 1.5 3.0
[1] 3wqr.a - 0
0
0.3 0.2 0.3 0.1 0.4 0.1 0.1 0.1 0.1 0.1 0.6 0.1 0.3 0.5 1.7 2.5
[1] 3wqs.b - 0.1 0.1
0.2
0.1 0.1 1.6 1.9 3.5 1.6 3.4 1.3 1.5 2.5 2.8 0.2 0.3 0.6 0.7
[1] 4gae.b - 0 0.2 0.6
0
0.1 0.7 1.2 3.5 1.1 2.4 0.5 0.7 1.9 1.6 0.3 0.1 0.6 0.6
[1] 4kp7.a - 0.1 0.8 1.4 0.1
0.2
1.2 1.3 3.9 1.5 2.9 1.3 1.1 2.1 2.5 0.3 0.1 0.7 0.7
[1] 4y67.a - 0.3 0.8 1.5 0.1 0.2
0
0.3 2.5 0 1.3 0 0 0.4 0.5 0.2 0.2 1.2 1.6
[1] 4y6p.a - 0.1 0.3 1.0 0.1 0.3 0.1
0.1
2.5 0.1 1.5 0.1 0.1 0.5 0.7 0.2 0.1 2.2 2.7
[1] 5jaz.a - 0.6 1.6 3.2 0.3 0.2 0.1 0.3
0
0 0 0 0.1 0.2 0 0.2 0.2 1.2 1.3
[1] 5jbi.a - 0.2 0.6 1.1 0.1 0.2 0.1 0.3 2.0
0
0.8 0 0 0.3 0.3 0.2 0.1 1.4 1.6
[1] 5jc1.a - 1.0 2.5 2.9 0.3 0.2 0 0.2 0.1 0
0
0 0 0.4 0 0.2 0.2 1.3 1.3
[1] 5jmp.a - 0.3 0.6 1.3 0.1 0.2 0 0.2 2.2 0 0.8
0
0 0.3 0.3 0.2 0.1 1.2 1.6
[1] 5jmw.a - 0.2 0.4 1.3 0.1 0.3 0.1 0.3 3.3 0 1.6 0.1
0
0.4 0.9 0.2 0.1 2.3 3.0
[1] 5jnl.a - 0.5 1.0 1.3 0.1 0.2 0.1 0.2 1.4 0 0.8 0 0
0.2
0.3 0.2 0.2 1.2 1.5
[1] 5jo0.a - 0.8 2.0 2.8 0.1 0.2 0.1 0.2 0 0 0 0 0 0.3
0
0.2 0.1 1.2 1.5
[2] 3au9.a - 3.7 4.1 5.0 2.9 3.7 6.0 6.1 6.9 5.9 5.8 6.2 6.0 6.5 6.2
0.1
0.1 3.1 4.0
[2] 3aua.b - 3.4 3.8 4.8 2.8 2.7 6.4 6.1 7.3 6.2 6.4 6.3 6.4 6.9 7.0 0
0
2.8 3.7
[2] 4y6r.a - 2.6 3.6 4.7 2.2 2.5 6.4 6.4 7.8 6.4 7.2 6.1 6.2 6.6 6.6 0.3 0.1
0.2
0.3
[2] 4y6s.a - 2.2 2.6 3.8 2.0 2.3 6.2 6.5 7.6 6.7 7.4 6.7 6.5 7.3 6.4 0 0.1 0.1
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3au8.a
3wqq.a
3wqr.a
3wqs.b
4gae.b
4kp7.a
4y67.a
4y6p.a
5jaz.a
5jbi.a
5jc1.a
5jmp.a
5jmw.a
5jnl.a
5jo0.a
3au9.a
3aua.b
4y6r.a
4y6s.a
[1] 3au8.a
0
.15 .13 .22 .20 .26 .21 .25 .18 .18 .16 .19 .29 .17 .17 .49 .50 .40 .37
[1] 3wqq.a .15
0
.05 .09 .09 .13 .11 .13 .09 .08 .07 .09 .18 .11 .07 .38 .41 .35 .30
[1] 3wqr.a .13 .05
0
.11 .11 .16 .13 .17 .10 .10 .08 .11 .20 .12 .09 .40 .42 .36 .33
[1] 3wqs.b .22 .09 .11
0
.04 .10 .17 .19 .10 .17 .10 .17 .17 .20 .11 .33 .36 .31 .25
[1] 4gae.b .20 .09 .11 .04
0
.09 .15 .15 .08 .16 .09 .15 .14 .19 .08 .30 .33 .31 .26
[1] 4kp7.a .26 .13 .16 .10 .09
0
.12 .17 .14 .15 .14 .13 .15 .16 .15 .26 .28 .22 .17
[1] 4y67.a .21 .11 .13 .17 .15 .12
0
.11 .08 .04 .07 .02 .11 .06 .07 .35 .36 .31 .27
[1] 4y6p.a .25 .13 .17 .19 .15 .17 .11
0
.14 .12 .12 .11 .08 .15 .11 .28 .30 .37 .33
[1] 5jaz.a .18 .09 .10 .10 .08 .14 .08 .14
0
.09 .03 .09 .12 .13 .04 .37 .38 .33 .30
[1] 5jbi.a .18 .08 .10 .17 .16 .15 .04 .12 .09
0
.08 .02 .12 .04 .08 .38 .39 .34 .30
[1] 5jc1.a .16 .07 .08 .10 .09 .14 .07 .12 .03 .08
0
.07 .13 .11 .01 .38 .38 .33 .30
[1] 5jmp.a .19 .09 .11 .17 .15 .13 .02 .11 .09 .02 .07
0
.12 .05 .07 .37 .37 .32 .29
[1] 5jmw.a .29 .18 .20 .17 .14 .15 .11 .08 .12 .12 .13 .12
0
.15 .12 .30 .30 .35 .31
[1] 5jnl.a .17 .11 .12 .20 .19 .16 .06 .15 .13 .04 .11 .05 .15
0
.12 .40 .40 .35 .32
[1] 5jo0.a .17 .07 .09 .11 .08 .15 .07 .11 .04 .08 .01 .07 .12 .12
0
.37 .38 .35 .31
[2] 3au9.a .49 .38 .40 .33 .30 .26 .35 .28 .37 .38 .38 .37 .30 .40 .37
0
.05 .21 .18
[2] 3aua.b .50 .41 .42 .36 .33 .28 .36 .30 .38 .39 .38 .37 .30 .40 .38 .05
0
.18 .17
[2] 4y6r.a .40 .35 .36 .31 .31 .22 .31 .37 .33 .34 .33 .32 .35 .35 .35 .21 .18
0
.07
[2] 4y6s.a .37 .30 .33 .25 .26 .17 .27 .33 .30 .30 .30 .29 .31 .32 .31 .18 .17 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
3au8.a
3wqq.a
3wqr.a
3wqs.b
4gae.b
4kp7.a
4y67.a
4y6p.a
5jaz.a
5jbi.a
5jc1.a
5jmp.a
5jmw.a
5jnl.a
5jo0.a
3au9.a
3aua.b
4y6r.a
4y6s.a
[1] 3au8.a
0
0.9 0.9 1.0 0.9 0.8 0.7 0.7 0.7 0.7 0.7 0.7 0.8 0.7 0.7 1.0 1.1 0.8 0.8
[1] 3wqq.a 0.9
0
0.2 1.4 1.6 1.2 1.0 1.5 1.2 1.3 1.0 1.2 1.6 1.0 0.9 1.5 1.5 1.4 1.2
[1] 3wqr.a 0.9 0.2
0
1.4 1.6 1.2 1.0 1.5 1.2 1.3 1.0 1.1 1.5 1.0 0.9 1.4 1.5 1.3 1.2
[1] 3wqs.b 1.0 1.4 1.4
0
0.9 0.7 1.7 2.0 1.9 2.0 1.4 1.9 2.1 1.5 1.3 1.9 1.9 1.7 1.6
[1] 4gae.b 0.9 1.6 1.6 0.9
0
1.2 2.1 2.0 2.2 2.3 1.8 2.2 2.1 1.8 1.5 1.9 1.8 2.0 1.8
[1] 4kp7.a 0.8 1.2 1.2 0.7 1.2
0
1.3 1.6 1.6 1.5 1.1 1.5 1.7 1.1 1.1 1.5 1.5 1.3 1.2
[1] 4y67.a 0.7 1.0 1.0 1.7 2.1 1.3
0
1.4 0.4 0.7 0.4 0.3 1.4 0.4 1.0 1.6 1.7 1.2 1.2
[1] 4y6p.a 0.7 1.5 1.5 2.0 2.0 1.6 1.4
0
1.6 1.2 1.5 1.4 0.3 1.3 1.5 0.8 1.0 1.1 1.1
[1] 5jaz.a 0.7 1.2 1.2 1.9 2.2 1.6 0.4 1.6
0
0.8 0.5 0.3 1.6 0.6 1.1 1.9 2.0 1.6 1.6
[1] 5jbi.a 0.7 1.3 1.3 2.0 2.3 1.5 0.7 1.2 0.8
0
0.9 0.6 1.2 0.8 1.2 1.6 1.7 1.3 1.3
[1] 5jc1.a 0.7 1.0 1.0 1.4 1.8 1.1 0.4 1.5 0.5 0.9
0
0.6 1.5 0.3 0.8 1.7 1.8 1.4 1.3
[1] 5jmp.a 0.7 1.2 1.1 1.9 2.2 1.5 0.3 1.4 0.3 0.6 0.6
0
1.4 0.5 1.1 1.7 1.8 1.4 1.4
[1] 5jmw.a 0.8 1.6 1.5 2.1 2.1 1.7 1.4 0.3 1.6 1.2 1.5 1.4
0
1.3 1.6 0.8 1.0 1.1 1.1
[1] 5jnl.a 0.7 1.0 1.0 1.5 1.8 1.1 0.4 1.3 0.6 0.8 0.3 0.5 1.3
0
0.9 1.6 1.7 1.2 1.2
[1] 5jo0.a 0.7 0.9 0.9 1.3 1.5 1.1 1.0 1.5 1.1 1.2 0.8 1.1 1.6 0.9
0
1.6 1.7 1.6 1.4
[2] 3au9.a 1.0 1.5 1.4 1.9 1.9 1.5 1.6 0.8 1.9 1.6 1.7 1.7 0.8 1.6 1.6
0
0.3 0.9 1.0
[2] 3aua.b 1.1 1.5 1.5 1.9 1.8 1.5 1.7 1.0 2.0 1.7 1.8 1.8 1.0 1.7 1.7 0.3
0
0.9 1.0
[2] 4y6r.a 0.8 1.4 1.3 1.7 2.0 1.3 1.2 1.1 1.6 1.3 1.4 1.4 1.1 1.2 1.6 0.9 0.9
0
0.4
[2] 4y6s.a 0.8 1.2 1.2 1.6 1.8 1.2 1.2 1.1 1.6 1.3 1.3 1.4 1.1 1.2 1.4 1.0 1.0 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.2 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
3au8.a
3wqq.a
3wqr.a
3wqs.b
4gae.b
4kp7.a
4y67.a
4y6p.a
5jaz.a
5jbi.a
5jc1.a
5jmp.a
5jmw.a
5jnl.a
5jo0.a
3au9.a
3aua.b
4y6r.a
4y6s.a
[1] 3au8.a
0
1.2 1.2 1.3 1.1 1.1 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.2 1.3 1.1 1.1
[1] 3wqq.a 1.2
0
0.6 3.0 3.0 2.9 2.6 3.0 2.2 2.5 2.2 2.6 3.0 2.7 2.1 3.0 3.0 2.6 2.4
[1] 3wqr.a 1.2 0.6
0
3.0 3.0 2.8 2.5 2.9 2.2 2.4 2.1 2.5 2.9 2.6 2.0 2.9 2.9 2.5 2.3
[1] 3wqs.b 1.3 3.0 3.0
0
1.8 1.1 1.9 2.9 2.5 2.2 2.3 2.0 2.9 1.8 2.5 3.0 3.0 2.3 2.5
[1] 4gae.b 1.1 3.0 3.0 1.8
0
1.9 2.7 2.2 3.1 2.6 2.8 2.6 2.3 2.5 2.3 2.3 2.2 2.7 2.8
[1] 4kp7.a 1.1 2.9 2.8 1.1 1.9
0
1.6 2.4 2.2 1.9 1.9 1.7 2.5 1.7 2.2 2.5 2.6 2.0 2.3
[1] 4y67.a 1.0 2.6 2.5 1.9 2.7 1.6
0
2.5 1.4 1.1 1.4 0.5 2.4 0.8 2.2 2.8 2.9 1.9 2.0
[1] 4y6p.a 1.0 3.0 2.9 2.9 2.2 2.4 2.5
0
2.9 2.0 2.8 2.3 0.7 2.2 2.1 1.5 1.5 2.4 2.4
[1] 5jaz.a 1.0 2.2 2.2 2.5 3.1 2.2 1.4 2.9
0
1.8 1.0 1.3 2.9 1.7 2.1 3.0 3.1 2.2 2.4
[1] 5jbi.a 1.0 2.5 2.4 2.2 2.6 1.9 1.1 2.0 1.8
0
1.8 1.1 1.9 0.9 2.0 2.5 2.6 1.9 1.9
[1] 5jc1.a 1.0 2.2 2.1 2.3 2.8 1.9 1.4 2.8 1.0 1.8
0
1.3 2.7 1.7 1.8 2.9 3.0 2.2 2.2
[1] 5jmp.a 1.0 2.6 2.5 2.0 2.6 1.7 0.5 2.3 1.3 1.1 1.3
0
2.3 0.9 2.1 2.8 2.8 1.9 2.2
[1] 5jmw.a 1.0 3.0 2.9 2.9 2.3 2.5 2.4 0.7 2.9 1.9 2.7 2.3
0
2.3 2.2 1.4 1.5 2.4 2.4
[1] 5jnl.a 1.0 2.7 2.6 1.8 2.5 1.7 0.8 2.2 1.7 0.9 1.7 0.9 2.3
0
2.2 2.8 2.8 1.9 2.1
[1] 5jo0.a 1.0 2.1 2.0 2.5 2.3 2.2 2.2 2.1 2.1 2.0 1.8 2.1 2.2 2.2
0
2.3 2.3 2.4 2.3
[2] 3au9.a 1.2 3.0 2.9 3.0 2.3 2.5 2.8 1.5 3.0 2.5 2.9 2.8 1.4 2.8 2.3
0
0.5 2.1 2.1
[2] 3aua.b 1.3 3.0 2.9 3.0 2.2 2.6 2.9 1.5 3.1 2.6 3.0 2.8 1.5 2.8 2.3 0.5
0
2.0 2.1
[2] 4y6r.a 1.1 2.6 2.5 2.3 2.7 2.0 1.9 2.4 2.2 1.9 2.2 1.9 2.4 1.9 2.4 2.1 2.0
0
0.9
[2] 4y6s.a 1.1 2.4 2.3 2.5 2.8 2.3 2.0 2.4 2.4 1.9 2.2 2.2 2.4 2.1 2.3 2.1 2.1 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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