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BMRR_BACSU_120_278

Multidrug-efflux transporter 1 regulator

Composition of the binding site

Protein chains monomer
A1 (BMRR_BACSU):142, 144:159, 170:172, 182, 187, 190, 224, 226, 229, 253:255, 266, 268142, 144:159, 170:172, 182, 187, 190, 224, 226, 229, 253:255, 266, 268

Full PDB list

1bow, 1exi, 1exj, 1r8e, 2bow, 3d6y, 3d6z, 3d70, 3d71, 3iao, 3q1m, 3q2y, 3q3d, 3q5p, 3q5r, 3q5s (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
4
2
P
1
4
4
E
1
4
5
V
1
4
7
L
1
4
8
N
1
4
9
Y
1
5
2
Y
1
7
0
G
1
7
1
A
1
7
2
I
1
8
2
Y
1
8
7
I
1
9
0
F
2
2
4
P
2
2
6
Y
2
2
9
E
2
5
3
I
2
5
5
E
2
6
6
Y
2
6
8
[1]1exi.a 118,sb25 . . . . . . . . . . . . . . . . . . . .
[1]3d6y.a ber25 . . . . . . . . . . . . . . . . . . . .
[1]3d6z.a rhq33 . . . . . . . . . . . . . . . . . . . .
[1]3d70.a none . . . . . . . . . . . . . . . . A . . .
[1]3iao.a none . . . . . . . . . . . . . . . . Q . . .
[1]3q1m.a m4a12 L . . . . . . . . . . . . . . . . . . .
[1]3q2y.a et24 L . . . . . . . . . . . . . . . . . . .
[1]3q3d.a puy34 L . . . . . . . . . . . . . . . . . . .
[1]3q5p.a tac32 L . . . . . . . . . . . . . . . . . . .
[1]3q5r.a kan33 L . . . . . . . . . . . . . . . . . . .
[1]3q5s.a ach10 L . . . . . . . . . . . . . . . . . . .
[2]2bow.a p4p25 . . . . . . . . . . . . . . . . . . - .
[3]1bow.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

[download in TSV format]
   
PDB.ch
A1
I
1
4
2
P
1
4
4
E
1
4
5
N
1
4
6
V
1
4
7
L
1
4
8
N
1
4
9
A
1
5
0
S
1
5
1
Y
1
5
2
S
1
5
3
K
1
5
4
L
1
5
5
K
1
5
6
K
1
5
7
F
1
5
8
I
1
5
9
Y
1
7
0
G
1
7
1
A
1
7
2
I
1
8
2
Y
1
8
7
I
1
9
0
F
2
2
4
P
2
2
6
Y
2
2
9
E
2
5
3
L
2
5
4
I
2
5
5
E
2
6
6
Y
2
6
8
[1]1exi.a . . . . . * . . * * . . . . . . . . . . . . . . . . . . . . .
[1]3d6y.a . . . . * * . . * * . . . . . . . * . . . . . . . . . . . . .
[1]3d6z.a . . . . * * . . * * . . . . . . . * . . . . . . . . . . . . .
[1]3d70.a . . . . * * . . * * . . . . . . . * . . . . . . . . A . . . .
[1]3iao.a . . . . . * . . * * . . . . . . . * . . . . . . . . Q . * . .
[1]3q1m.a L . . . * * * . * * . . . . . . . * . . . . . . . . . . . . *
[1]3q2y.a L . . . * * . . * * . . . . . . . * . . . . . . . . . . . . .
[1]3q3d.a L . . . * * . . * * . . . . . . . * . . . . . . . . . . . . .
[1]3q5p.a L . . . * * . . * * . . . . . . . * . . . . . . . . . . . . .
[1]3q5r.a L . . . * * . . * * . . . . . . . * . . . . . . . . . . . . .
[1]3q5s.a L . . . * * . . * * . . . . . . . * . . . . . . . . . . . . .
[2]2bow.a . . . . * * . . . . - - - - - - - * . . . . . . . . . . * - .
[3]1bow.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
1exi.a:118,sb
3d6y.a:ber
3d6z.a:rhq
3d70.a is apo
3iao.a is apo
3q1m.a:m4a
3q2y.a:et
3q3d.a:puy
3q5p.a:tac
3q5r.a:kan
3q5s.a:ach
2bow.a:p4p
1bow.a is apo
[1] 1exi.a
0.1
0.2 0.4 - - 0 0.2 0.3 0.3 0.1 0.1 8.6 -
[1] 3d6y.a 0.3
0
0.1 - - 0.1 0 0.4 0.2 0.1 0 9.3 -
[1] 3d6z.a 0.1 0
0
- - 0 0 0.2 0.2 0 0 9.8 -
[1] 3d70.a 0.9 0.7 1.5
-
- 0 0.4 0.6 0.9 1.2 0.3 10 -
[1] 3iao.a 0.9 0.3 0.3 -
-
0.1 0.2 0.8 0.3 0.3 0.6 9.5 -
[1] 3q1m.a 0.4 0.7 0.8 - -
0
0.2 1.3 0.9 0.7 0.3 9.6 -
[1] 3q2y.a 0.1 0 0.4 - - 0
0
0.3 0.3 0.1 0.1 9.5 -
[1] 3q3d.a 0.1 0 0.4 - - 0 0
0.1
0.2 0.1 0.1 9.1 -
[1] 3q5p.a 0.1 0.1 0.2 - - 0 0 0.1
0.2
0.2 0 9.2 -
[1] 3q5r.a 0.1 0 0.2 - - 0.1 0 0.2 0.2
0.2
0.3 8.9 -
[1] 3q5s.a 0.4 0 0.2 - - 0.1 0 0.2 0.3 0
0.1
8.4 -
[2] 2bow.a 5.2 3.1 3.3 - - 0.7 2.9 4.2 2.5 4.0 1.3
0.1
-
[3] 1bow.a 14 9.7 15 - - 6.7 11 14 14 14 6.8 15
-
[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
1exi.a
3d6y.a
3d6z.a
3d70.a
3iao.a
3q1m.a
3q2y.a
3q3d.a
3q5p.a
3q5r.a
3q5s.a
2bow.a
1bow.a
[1] 1exi.a
0
.09 .10 .14 .12 .12 .09 .08 .08 .11 .09 .34 .76
[1] 3d6y.a .09
0
.04 .11 .07 .08 .03 .04 .04 .06 .06 .33 .76
[1] 3d6z.a .10 .04
0
.08 .06 .10 .04 .05 .03 .05 .07 .33 .76
[1] 3d70.a .14 .11 .08
0
.10 .12 .10 .12 .10 .11 .13 .33 .75
[1] 3iao.a .12 .07 .06 .10
0
.12 .08 .09 .08 .08 .09 .32 .76
[1] 3q1m.a .12 .08 .10 .12 .12
0
.09 .09 .09 .08 .08 .35 .75
[1] 3q2y.a .09 .03 .04 .10 .08 .09
0
.01 .02 .05 .08 .34 .76
[1] 3q3d.a .08 .04 .05 .12 .09 .09 .01
0
.02 .05 .06 .35 .77
[1] 3q5p.a .08 .04 .03 .10 .08 .09 .02 .02
0
.04 .05 .34 .77
[1] 3q5r.a .11 .06 .05 .11 .08 .08 .05 .05 .04
0
.04 .31 .79
[1] 3q5s.a .09 .06 .07 .13 .09 .08 .08 .06 .05 .04
0
.32 .81
[2] 2bow.a .34 .33 .33 .33 .32 .35 .34 .35 .34 .31 .32
0
.88
[3] 1bow.a .76 .76 .76 .75 .76 .75 .76 .77 .77 .79 .81 .88
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
1exi.a
3d6y.a
3d6z.a
3d70.a
3iao.a
3q1m.a
3q2y.a
3q3d.a
3q5p.a
3q5r.a
3q5s.a
2bow.a
1bow.a
[1] 1exi.a
0
0.7 0.7 0.7 0.8 0.7 0.7 0.7 0.7 0.6 0.7 5.9 6.8
[1] 3d6y.a 0.7
0
0.2 0.4 0.5 0.4 0.3 0.3 0.4 0.4 0.4 5.9 6.7
[1] 3d6z.a 0.7 0.2
0
0.5 0.6 0.5 0.3 0.3 0.3 0.3 0.3 6.0 6.8
[1] 3d70.a 0.7 0.4 0.5
0
0.7 0.4 0.5 0.5 0.5 0.6 0.6 6.0 6.8
[1] 3iao.a 0.8 0.5 0.6 0.7
0
0.7 0.6 0.6 0.6 0.6 0.7 6.0 6.9
[1] 3q1m.a 0.7 0.4 0.5 0.4 0.7
0
0.4 0.5 0.5 0.5 0.5 5.9 6.7
[1] 3q2y.a 0.7 0.3 0.3 0.5 0.6 0.4
0
0.3 0.3 0.3 0.3 6.0 6.8
[1] 3q3d.a 0.7 0.3 0.3 0.5 0.6 0.5 0.3
0
0.3 0.3 0.3 5.9 6.7
[1] 3q5p.a 0.7 0.4 0.3 0.5 0.6 0.5 0.3 0.3
0
0.3 0.3 6.0 6.8
[1] 3q5r.a 0.6 0.4 0.3 0.6 0.6 0.5 0.3 0.3 0.3
0
0.2 5.9 6.8
[1] 3q5s.a 0.7 0.4 0.3 0.6 0.7 0.5 0.3 0.3 0.3 0.2
0
5.9 6.8
[2] 2bow.a 5.9 5.9 6.0 6.0 6.0 5.9 6.0 5.9 6.0 5.9 5.9
0
3.5
[3] 1bow.a 6.8 6.7 6.8 6.8 6.9 6.7 6.8 6.7 6.8 6.8 6.8 3.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
1exi.a
3d6y.a
3d6z.a
3d70.a
3iao.a
3q1m.a
3q2y.a
3q3d.a
3q5p.a
3q5r.a
3q5s.a
2bow.a
1bow.a
[1] 1exi.a
0
1.1 1.0 1.4 1.3 1.2 1.3 1.3 1.2 1.1 1.2 5.5 7.1
[1] 3d6y.a 1.1
0
0.6 1.0 1.0 0.8 0.8 0.9 0.9 0.7 0.8 5.4 6.9
[1] 3d6z.a 1.0 0.6
0
1.1 1.1 1.0 1.0 1.0 1.0 0.8 0.9 5.4 7.0
[1] 3d70.a 1.4 1.0 1.1
0
1.0 0.8 0.9 0.9 1.1 1.0 1.1 5.5 7.1
[1] 3iao.a 1.3 1.0 1.1 1.0
0
1.1 1.0 0.9 1.1 1.1 1.2 5.5 7.1
[1] 3q1m.a 1.2 0.8 1.0 0.8 1.1
0
0.8 0.8 0.9 0.9 1.0 5.4 6.6
[1] 3q2y.a 1.3 0.8 1.0 0.9 1.0 0.8
0
0.6 0.8 0.5 0.8 5.5 7.0
[1] 3q3d.a 1.3 0.9 1.0 0.9 0.9 0.8 0.6
0
0.6 0.7 0.9 5.4 7.0
[1] 3q5p.a 1.2 0.9 1.0 1.1 1.1 0.9 0.8 0.6
0
0.8 1.0 5.5 6.7
[1] 3q5r.a 1.1 0.7 0.8 1.0 1.1 0.9 0.5 0.7 0.8
0
0.6 5.4 6.8
[1] 3q5s.a 1.2 0.8 0.9 1.1 1.2 1.0 0.8 0.9 1.0 0.6
0
5.4 6.7
[2] 2bow.a 5.5 5.4 5.4 5.5 5.5 5.4 5.5 5.4 5.5 5.4 5.4
0
3.1
[3] 1bow.a 7.1 6.9 7.0 7.1 7.1 6.6 7.0 7.0 6.7 6.8 6.7 3.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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