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DXR_MYCTU_1_390

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

Composition of the binding site

Protein chains monomer
A1 (DXR_MYCTU):18:25, 45:50, 67, 69, 85, 87, 88, 103:105, 108, 126:129, 151:153, 176, 177, 200:207, 209, 210, 213, 218, 219, 222, 245, 248, 265, 26718:25, 45:50, 67, 69, 85, 87, 88, 103:105, 108, 126:129, 151:153, 176, 177, 200:207, 209, 210, 213, 218, 219, 222, 245, 248, 265, 267
Metals (Me):Mn

Full PDB list

2c82, 2jcv, 2jcx, 2jcy, 2jd0, 2jd1, 2jd2, 2y1c, 2y1d, 2y1e, 2y1f, 2y1g, 3ras, 3zhx, 3zhy, 3zhz, 3zi0, 4a03, 4aic, 4ooe, 4oof, 4rcv (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
G
1
9
T
2
1
G
2
2
S
2
3
I
2
4
A
4
6
G
4
7
G
4
8
A
4
9
H
5
0
A
6
9
A
1
0
3
L
1
0
4
V
1
0
5
L
1
0
8
A
1
2
6
N
1
2
7
K
1
2
8
E
1
2
9
D
1
5
1
S
1
5
2
E
1
5
3
A
1
7
6
S
1
7
7
H
2
0
0
W
2
0
3
M
2
0
5
G
2
0
6
P
2
0
7
N
2
0
9
T
2
1
0
S
2
1
3
N
2
1
8
K
2
1
9
E
2
2
2
S
2
4
5
H
2
4
8
P
2
6
5
M
2
6
7
[1]2y1d.a 34f19 . . . . . . . . . . - . . . . . . . . . . . . . - - - - - . . . . . . . . . . Mn
[1]2y1f.a 34f,ndp67 . . . . . . . . . . . . . . . . . . . . . . . . - - . . . . . . . . . . . . . Mn
[1]2y1g.a fm520 . . . . . . . . . . . . . . . . . . . . . . . . - - . . . . . . . . . . . . . Mn
[1]3ras.a dcv,fm5,ndp88 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]3zhx.a fm625 . . . . . . . . . . . . . . . . . . . . . . . . - - - - . . . . . . . . . . . Mn
[1]3zhy.a fm6,ndp73 . . . . . . . . . . . . . . . . . . . . . . . . - - . . . . . . . . . . . . . Mn
[1]3zhz.a fm736 . . . . . . . . . . . . . . . . . . . . . . . . . - - - - . . . . . . . . . .
[1]3zi0.a fm831 . . . . . . . . . . - . . . . . . . . . . . . . - - - - . . . . . . . . . . .
[1]4rcv.a de2,ndp55 . . . . . . . . . . . . . . . . . . . . . . . . - - - - . . . . . . . . . . . Mn
[2]2jcv.a fom,ndp59 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2jcx.a fom,ndp50 . . . . . . . . . . . . . . . . . . . N . . . . . . . . . . . . . . Q . . . .
[2]2jcy.a none . . . . . . . . . . . . . . . . . . . N . . . . . . . . . . . . . . Q . . . .
[2]2jd0.a ndp27 . . . . . . . . . . . . . . . . . . . N . . . . . . . . . . . . . . Q . . . .
[2]2jd1.a ndp48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[2]2jd2.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[2]4a03.a f98,ndp60 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[2]4ooe.c fom,ndp59 . . . . . . . . . . . . . . . . . . . . . . . . . Y . . . . . . . . . . . . . Mn
[2]4oof.a fom,ndp59 . . . . . . . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . . . . 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
L
1
8
G
1
9
S
2
0
T
2
1
G
2
2
S
2
3
I
2
4
G
2
5
A
4
5
A
4
6
G
4
7
G
4
8
A
4
9
H
5
0
A
6
7
A
6
9
S
8
5
A
8
7
A
8
8
A
1
0
3
L
1
0
4
V
1
0
5
L
1
0
8
A
1
2
6
N
1
2
7
K
1
2
8
E
1
2
9
D
1
5
1
S
1
5
2
E
1
5
3
A
1
7
6
S
1
7
7
H
2
0
0
P
2
0
1
T
2
0
2
W
2
0
3
S
2
0
4
M
2
0
5
G
2
0
6
P
2
0
7
N
2
0
9
T
2
1
0
S
2
1
3
N
2
1
8
K
2
1
9
E
2
2
2
S
2
4
5
H
2
4
8
P
2
6
5
M
2
6
7
[1]2y1d.a . . . . . . . . . . . . . . . - . . . . . . * . . . . . . . . . - - - - - - - - . . . . . . . . . . Mn
[1]2y1f.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - * . . . . . . . . . . . . Mn
[1]2y1g.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - . * . . . . . . . . . . . . Mn
[1]3ras.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . * . . . . . . . . . . . . Mn
[1]3zhx.a . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . - - - - - - - . . . . . . . . . . . Mn
[1]3zhy.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - . * . . . . . . . . . . . . Mn
[1]3zhz.a . . . . . . . . . . * . . . . . . . . . . . * . . . . . . . . . . . - - - - - - . . . . . . . . . .
[1]3zi0.a . . . . . . . . . . . . . . . - . . . . . . * . . . . . . . . . - - - - - - - . . . . . . . . . . .
[1]4rcv.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - - . . . . . . . . . . . Mn
[2]2jcv.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . * . * . . . . . . . . . . . .
[2]2jcx.a . . . . . . . . . . . . . . . . . . . . . . . . . . . N . . . . * . . * . * . . . . . . . Q . . . .
[2]2jcy.a . . . . . . . . . . . . . . . . . . . . . . * . . . . N . . . . . . * * . * . . . . . . . Q . . . .
[2]2jd0.a . . . . . . . . . . . . . . . . . . . . . . . . . . . N . . . . * . * * . * . . . . . . . Q . . . .
[2]2jd1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . * . * . . . . . . . . . . . . Mn
[2]2jd2.a . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . * . . * . * . . . . . . . . . . . . Mn
[2]4a03.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . * . * . . . . . . . . . . . . Mn
[2]4ooe.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . Y . * . . . . . . . . . . . . Mn
[2]4oof.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . * F . * . . . . . . . . . . . . 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
2y1d.a:34f
2y1f.a:34f,ndp
2y1g.a:fm5
3ras.a:dcv,fm5,ndp
3zhx.a:fm6
3zhy.a:fm6,ndp
3zhz.a:fm7
3zi0.a:fm8
4rcv.a:de2,ndp
2jcv.a:fom,ndp
2jcx.a:fom,ndp
2jcy.a is apo
2jd0.a:ndp
2jd1.a:ndp
2jd2.a is apo
4a03.a:f98,ndp
4ooe.c:fom,ndp
4oof.a:fom,ndp
[1] 2y1d.a
0
1.4 0 1.5 0 0.7 0.4 0.2 1.3 1.0 0.8 - 0.6 1.0 - 1.0 1.3 1.3
[1] 2y1f.a 0
0
0.1 0.1 0.2 0.3 3.5 1.4 0.5 0.7 0.4 - 0.1 0 - 0.3 0.9 0.7
[1] 2y1g.a 0 1.0
0
1.3 0.1 1.1 3.5 1.2 1.2 1.5 1.2 - 0.3 0.9 - 1.2 2.3 1.7
[1] 3ras.a 0.1 0.6 0
0.3
0.4 0.5 4.4 3.8 1.1 0.7 0.2 - 0.3 0.6 - 0.1 0.6 0.4
[1] 3zhx.a 0.2 1.8 0.3 2.2
0
1.5 0.8 0.2 1.7 1.3 1.6 - 0.8 1.3 - 1.7 1.4 1.7
[1] 3zhy.a 0.1 0.2 0.1 0.4 0.3
0.1
3.3 1.6 0.3 0.5 0.4 - 0.2 0.4 - 0.2 0.4 0.3
[1] 3zhz.a 0.1 3.6 0.1 3.9 0.1 3.3
0
0.3 2.7 3.6 3.6 - 2.6 3.3 - 3.6 2.3 3.9
[1] 3zi0.a 0.1 1.9 0.2 2.3 0.1 2.3 0.6
0.1
2.4 2.7 2.4 - 1.6 2.1 - 2.1 2.1 2.3
[1] 4rcv.a 0.1 0.3 0.1 0.6 0.2 0.2 0.7 0
0
0.5 0.3 - 0.3 0.1 - 0.3 0.4 0.2
[2] 2jcv.a 4.1 6.2 5.1 5.2 6.3 8.0 11 11 1.0
0.1
0.1 - 0.3 0.2 - 0.2 0.6 0.3
[2] 2jcx.a 4.0 5.1 4.7 5.5 6.3 8.2 11 10 0.9 0.2
0
- 0.1 0.3 - 0.1 0.7 0.7
[2] 2jcy.a 3.7 6.7 4.3 7.3 6.5 10 11 9.9 3.6 4.5 3.1
-
0.4 2.5 - 4.8 5.0 5.2
[2] 2jd0.a 2.9 3.9 3.0 4.2 6.0 7.1 8.3 9.7 0.5 0.7 0.2 -
0
0.2 - 0.7 1.0 0.8
[2] 2jd1.a 4.5 5.1 4.7 5.0 6.8 7.5 11 12 0.4 0.3 0.4 - 0
0
- 0.2 1.0 0.6
[2] 2jd2.a 3.6 6.5 4.2 6.2 6.5 8.7 8.7 9.2 1.8 2.2 1.7 - 0.4 1.6
-
2.0 2.9 2.6
[2] 4a03.a 4.3 5.7 4.8 5.3 6.3 7.7 10 11 1.2 0.7 0.4 - 0.4 0.5 -
0.1
0.7 0.4
[2] 4ooe.c 3.8 7.5 4.6 6.5 5.3 7.3 10 10 2.1 1.7 1.5 - 1.8 2.2 - 1.3
0.1
0.6
[2] 4oof.a 4.0 5.3 4.4 4.7 5.8 6.4 10 11 1.3 0.8 0.5 - 0.7 0.9 - 0.1 0.2
0.1
[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
2y1d.a
2y1f.a
2y1g.a
3ras.a
3zhx.a
3zhy.a
3zhz.a
3zi0.a
4rcv.a
2jcv.a
2jcx.a
2jcy.a
2jd0.a
2jd1.a
2jd2.a
4a03.a
4ooe.c
4oof.a
[1] 2y1d.a
0
.09 .09 .15 .03 .09 .07 .04 .05 .28 .28 .25 .24 .29 .23 .29 .31 .29
[1] 2y1f.a .09
0
.03 .07 .12 .04 .15 .12 .08 .21 .21 .24 .19 .21 .24 .21 .26 .23
[1] 2y1g.a .09 .03
0
.09 .10 .04 .15 .11 .10 .22 .22 .23 .19 .22 .22 .23 .27 .25
[1] 3ras.a .15 .07 .09
0
.17 .08 .19 .16 .13 .17 .17 .29 .17 .19 .22 .15 .19 .17
[1] 3zhx.a .03 .12 .10 .17
0
.11 .06 .05 .06 .29 .29 .27 .25 .30 .24 .31 .32 .31
[1] 3zhy.a .09 .04 .04 .08 .11
0
.14 .11 .07 .21 .21 .24 .19 .22 .24 .21 .24 .22
[1] 3zhz.a .07 .15 .15 .19 .06 .14
0
.09 .10 .30 .31 .32 .30 .34 .29 .32 .31 .32
[1] 3zi0.a .04 .12 .11 .16 .05 .11 .09
0
.06 .30 .30 .27 .25 .30 .24 .31 .33 .30
[1] 4rcv.a .05 .08 .10 .13 .06 .07 .10 .06
0
.26 .27 .28 .24 .26 .25 .26 .28 .26
[2] 2jcv.a .28 .21 .22 .17 .29 .21 .30 .30 .26
0
.01 .20 .07 .06 .10 .04 .09 .08
[2] 2jcx.a .28 .21 .22 .17 .29 .21 .31 .30 .27 .01
0
.19 .07 .06 .10 .05 .10 .09
[2] 2jcy.a .25 .24 .23 .29 .27 .24 .32 .27 .28 .20 .19
0
.17 .18 .14 .20 .23 .22
[2] 2jd0.a .24 .19 .19 .17 .25 .19 .30 .25 .24 .07 .07 .17
0
.06 .08 .08 .10 .09
[2] 2jd1.a .29 .21 .22 .19 .30 .22 .34 .30 .26 .06 .06 .18 .06
0
.10 .07 .11 .07
[2] 2jd2.a .23 .24 .22 .22 .24 .24 .29 .24 .25 .10 .10 .14 .08 .10
0
.11 .14 .13
[2] 4a03.a .29 .21 .23 .15 .31 .21 .32 .31 .26 .04 .05 .20 .08 .07 .11
0
.07 .06
[2] 4ooe.c .31 .26 .27 .19 .32 .24 .31 .33 .28 .09 .10 .23 .10 .11 .14 .07
0
.06
[2] 4oof.a .29 .23 .25 .17 .31 .22 .32 .30 .26 .08 .09 .22 .09 .07 .13 .06 .06
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
2y1d.a
2y1f.a
2y1g.a
3ras.a
3zhx.a
3zhy.a
3zhz.a
3zi0.a
4rcv.a
2jcv.a
2jcx.a
2jcy.a
2jd0.a
2jd1.a
2jd2.a
4a03.a
4ooe.c
4oof.a
[1] 2y1d.a
0
0.5 0.4 0.7 0.4 0.7 0.8 1.0 0.7 0.8 0.6 0.4 0.4 0.5 0.4 0.8 1.3 0.9
[1] 2y1f.a 0.5
0
0.5 0.5 0.7 0.5 0.9 1.1 0.4 0.6 0.5 0.8 0.6 0.3 0.7 0.6 1.2 0.7
[1] 2y1g.a 0.4 0.5
0
0.7 0.5 0.7 0.9 1.0 0.6 0.8 0.6 0.8 0.6 0.6 0.8 0.8 1.3 0.9
[1] 3ras.a 0.7 0.5 0.7
0
0.9 0.5 3.2 1.4 0.4 1.2 1.2 1.6 1.3 1.3 1.4 1.2 1.5 1.3
[1] 3zhx.a 0.4 0.7 0.5 0.9
0
0.8 0.8 1.0 0.8 0.9 0.7 0.4 0.5 0.7 0.4 1.0 1.4 1.0
[1] 3zhy.a 0.7 0.5 0.7 0.5 0.8
0
0.8 1.5 0.4 0.4 0.4 0.9 0.7 0.4 0.7 0.4 0.8 0.4
[1] 3zhz.a 0.8 0.9 0.9 3.2 0.8 0.8
0
1.6 0.8 3.4 3.4 3.0 3.5 3.5 3.5 3.4 3.5 3.5
[1] 3zi0.a 1.0 1.1 1.0 1.4 1.0 1.5 1.6
0
1.4 1.5 1.3 0.9 0.9 1.2 1.1 1.5 2.0 1.6
[1] 4rcv.a 0.7 0.4 0.6 0.4 0.8 0.4 0.8 1.4
0
0.4 0.4 0.8 0.6 0.3 0.6 0.4 0.9 0.5
[2] 2jcv.a 0.8 0.6 0.8 1.2 0.9 0.4 3.4 1.5 0.4
0
0.3 1.3 0.8 0.4 0.8 0.3 0.7 0.4
[2] 2jcx.a 0.6 0.5 0.6 1.2 0.7 0.4 3.4 1.3 0.4 0.3
0
1.2 0.7 0.3 0.7 0.4 0.9 0.5
[2] 2jcy.a 0.4 0.8 0.8 1.6 0.4 0.9 3.0 0.9 0.8 1.3 1.2
0
1.0 1.1 1.0 1.4 1.7 1.4
[2] 2jd0.a 0.4 0.6 0.6 1.3 0.5 0.7 3.5 0.9 0.6 0.8 0.7 1.0
0
0.6 0.4 0.9 1.3 0.9
[2] 2jd1.a 0.5 0.3 0.6 1.3 0.7 0.4 3.5 1.2 0.3 0.4 0.3 1.1 0.6
0
0.6 0.5 1.0 0.6
[2] 2jd2.a 0.4 0.7 0.8 1.4 0.4 0.7 3.5 1.1 0.6 0.8 0.7 1.0 0.4 0.6
0
0.8 1.1 0.9
[2] 4a03.a 0.8 0.6 0.8 1.2 1.0 0.4 3.4 1.5 0.4 0.3 0.4 1.4 0.9 0.5 0.8
0
0.7 0.3
[2] 4ooe.c 1.3 1.2 1.3 1.5 1.4 0.8 3.5 2.0 0.9 0.7 0.9 1.7 1.3 1.0 1.1 0.7
0
0.5
[2] 4oof.a 0.9 0.7 0.9 1.3 1.0 0.4 3.5 1.6 0.5 0.4 0.5 1.4 0.9 0.6 0.9 0.3 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
2y1d.a
2y1f.a
2y1g.a
3ras.a
3zhx.a
3zhy.a
3zhz.a
3zi0.a
4rcv.a
2jcv.a
2jcx.a
2jcy.a
2jd0.a
2jd1.a
2jd2.a
4a03.a
4ooe.c
4oof.a
[1] 2y1d.a
0
1.1 1.0 1.2 0.8 1.2 1.2 1.1 1.2 1.3 1.2 0.8 1.0 1.1 0.9 1.3 1.6 1.4
[1] 2y1f.a 1.1
0
0.5 0.6 1.0 0.6 1.1 1.3 0.6 0.7 0.6 1.2 0.8 0.4 0.9 0.6 1.2 0.8
[1] 2y1g.a 1.0 0.5
0
0.8 0.8 0.8 1.1 1.1 0.8 0.9 0.8 1.2 0.8 0.7 0.9 0.9 1.3 1.0
[1] 3ras.a 1.2 0.6 0.8
0
1.1 0.6 3.6 1.5 0.6 1.6 1.7 2.4 1.8 1.7 1.9 1.6 1.7 1.5
[1] 3zhx.a 0.8 1.0 0.8 1.1
0
1.1 1.0 1.1 1.1 1.2 1.0 0.9 0.8 1.0 0.6 1.2 1.5 1.3
[1] 3zhy.a 1.2 0.6 0.8 0.6 1.1
0
1.0 1.6 0.6 0.6 0.6 1.4 0.9 0.5 1.0 0.5 0.8 0.5
[1] 3zhz.a 1.2 1.1 1.1 3.6 1.0 1.0
0
1.7 1.0 3.8 3.9 3.5 4.0 3.9 3.9 3.9 3.9 3.9
[1] 3zi0.a 1.1 1.3 1.1 1.5 1.1 1.6 1.7
0
1.6 1.7 1.5 1.1 1.1 1.4 1.2 1.7 2.1 1.8
[1] 4rcv.a 1.2 0.6 0.8 0.6 1.1 0.6 1.0 1.6
0
0.6 0.6 1.2 0.8 0.5 0.8 0.6 1.0 0.7
[2] 2jcv.a 1.3 0.7 0.9 1.6 1.2 0.6 3.8 1.7 0.6
0
0.4 2.1 1.0 0.6 1.0 0.5 0.8 0.6
[2] 2jcx.a 1.2 0.6 0.8 1.7 1.0 0.6 3.9 1.5 0.6 0.4
0
2.0 0.8 0.5 0.9 0.5 1.0 0.7
[2] 2jcy.a 0.8 1.2 1.2 2.4 0.9 1.4 3.5 1.1 1.2 2.1 2.0
0
1.8 2.0 1.8 2.1 2.3 2.2
[2] 2jd0.a 1.0 0.8 0.8 1.8 0.8 0.9 4.0 1.1 0.8 1.0 0.8 1.8
0
0.8 0.8 1.0 1.4 1.1
[2] 2jd1.a 1.1 0.4 0.7 1.7 1.0 0.5 3.9 1.4 0.5 0.6 0.5 2.0 0.8
0
0.8 0.5 1.0 0.7
[2] 2jd2.a 0.9 0.9 0.9 1.9 0.6 1.0 3.9 1.2 0.8 1.0 0.9 1.8 0.8 0.8
0
1.0 1.3 1.1
[2] 4a03.a 1.3 0.6 0.9 1.6 1.2 0.5 3.9 1.7 0.6 0.5 0.5 2.1 1.0 0.5 1.0
0
0.7 0.4
[2] 4ooe.c 1.6 1.2 1.3 1.7 1.5 0.8 3.9 2.1 1.0 0.8 1.0 2.3 1.4 1.0 1.3 0.7
0
0.5
[2] 4oof.a 1.4 0.8 1.0 1.5 1.3 0.5 3.9 1.8 0.7 0.6 0.7 2.2 1.1 0.7 1.1 0.4 0.5
0
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