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BLA1_STEMA_22_290

Metallo-beta-lactamase L1 type 3 [Metallo-beta-lactamase superfamily. Class-B beta-lactamase family]

Composition of the binding site

Protein chains monomer
A1 (BLA1_STEMA):30, 32, 34, 38, 105, 107, 109, 110, 142, 145, 148, 149, 181, 206, 208, 210, 212, 246, 24930, 32, 34, 38, 105, 107, 109, 110, 142, 145, 148, 149, 181, 206, 208, 210, 212, 246, 249
Metals (Me):Zn

Full PDB list

1sml, 2aio, 2fm6, 2fu6, 2fu7, 2fu8, 2fu9, 2gfj, 2gfk, 2h6a, 2hb9, 2qdt, 2qin, 2qjs, 5dpx, 5evb, 5evd, 5evk, 5hh5, 5hh6 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Y
3
2
V
3
4
W
3
8
H
1
0
5
H
1
0
7
D
1
0
9
H
1
1
0
F
1
4
5
G
1
4
8
I
1
4
9
H
1
8
1
S
2
0
6
S
2
0
8
P
2
1
0
Y
2
1
2
H
2
4
6
A
2
4
9
[1]1sml.a none . . . . . . . . . . . . . . . . . Zn
[1]2aio.a mx130 . . . . . . . . . . . . . . . . . Zn
[1]2fu8.a mco14 . . . . . . . . . . . . . . . . . Zn
[1]2fu9.a mp221 . . . . . . . . . . . . . . . . . Zn
[1]2gfj.a vi23 . . . . . . . . . . . . . . . . . Zn
[1]2gfk.b vii23 . . . . . . . . . . . . . . . . . Zn
[1]2hb9.a l1314 . . . . . . . . . . . . . . . . . Zn
[1]2qdt.a i3811 . . . . . . . . . . . . . . . . . Zn
[1]2qin.b none . . . . . C . . . . . . . . . . . Zn
[1]2qjs.a none - - - . . N . . . . . . . . . . . Zn
[1]5dpx.b l3b13 . . . . . . . . . . . . . . . . . Zn
[1]5evb.a 3r913 . . . . . . . . . . . . . . . . . Zn
[1]5evd.a vc215 . . . . . . . . . . . . . . . . . Zn
[1]5evk.a 3c713 . . . . . . . . . . . . . . . . . Zn
[1]5hh5.a 60m14 . . . . . . . . . . . . . . . . . Zn
[1]5hh6.a 60n15 . . . . . . . . . . . . . . . . . Zn

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
R
3
0
Y
3
2
V
3
4
W
3
8
H
1
0
5
H
1
0
7
D
1
0
9
H
1
1
0
D
1
4
2
F
1
4
5
G
1
4
8
I
1
4
9
H
1
8
1
S
2
0
6
S
2
0
8
P
2
1
0
Y
2
1
2
H
2
4
6
A
2
4
9
[1]1sml.a . * . . . . . . . * . . . . . . . . . Zn
[1]2aio.a . * . . . . . . . * . * . . . . . . . Zn
[1]2fu8.a . * . . . . . . . * . . . . . . . . . Zn
[1]2fu9.a . * . . . . . . . * . * . . . . . . . Zn
[1]2gfj.a . . . . . . . . . * . . . . . . . . . Zn
[1]2gfk.b . . . . . . . . . * . * . . . . . . . Zn
[1]2hb9.a . . . . . . . . . * . . . . . . . . . Zn
[1]2qdt.a . * . . . . . . . * . . . . . . . . . Zn
[1]2qin.b . * . . . . C . . * . * . . . . . . . Zn
[1]2qjs.a - - - - . . N . . * . * . . . . . . . Zn
[1]5dpx.b . * . . . . . . . . . . . . . . . . . Zn
[1]5evb.a . * . . . . . . . * . * . . . . . . . Zn
[1]5evd.a . * . . . . . . . * . * . . . . . . . Zn
[1]5evk.a . * . . . . . . . * . . . . . . . . . Zn
[1]5hh5.a . * . . . . . . . * . . . . . . . . . Zn
[1]5hh6.a . * . . . . . . . * . . . . . . . . . Zn

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
1sml.a is apo
2aio.a:mx1
2fu8.a:mco
2fu9.a:mp2
2gfj.a:vi
2gfk.b:vii
2hb9.a:l13
2qdt.a:i38
2qin.b is apo
2qjs.a is apo
5dpx.b:l3b
5evb.a:3r9
5evd.a:vc2
5evk.a:3c7
5hh5.a:60m
5hh6.a:60n
[1] 1sml.a
-
0.6 0.1 0.3 2.2 2.5 2.7 0 - - 3.3 1.0 1.1 0 0.2 0.7
[1] 2aio.a -
0
0.2 0 2.3 2.5 2.6 0.1 - - 2.9 0.1 0.6 0 0.2 0.3
[1] 2fu8.a - 0.6
0
0.3 2.2 2.3 2.6 0 - - 2.9 0.8 1.0 0 0.2 0.2
[1] 2fu9.a - 0.2 0
0
2.7 2.7 2.7 0 - - 3.1 0.4 0.5 0.1 0.2 0.2
[1] 2gfj.a - 1.1 0 0.4
0
0 0.2 0 - - 2.4 1.0 1.1 0 0.4 0.6
[1] 2gfk.b - 0.7 0.1 0.1 0
0
0.2 0 - - 3.2 0.4 1.0 0 0.3 0.5
[1] 2hb9.a - 0.9 0.4 0.1 0.1 0.1
0
0.1 - - 3.1 0.9 0.9 0.1 0.1 0.2
[1] 2qdt.a - 0.6 0.1 0.3 2.0 2.0 2.7
0
- - 3.1 1.0 1.3 0 0.2 0.3
[1] 2qin.b - 0.4 0.1 0.1 2.6 2.8 2.7 0
-
- 3.0 0.5 0.5 0.1 0.1 0.3
[1] 2qjs.a - 0.1 0 0 0 0 0.1 0 -
-
3.1 0.5 0.5 0 0.1 0.2
[1] 5dpx.b - 0.6 0.1 0.1 2.0 2.0 2.1 0.1 - -
0
0.1 0.1 0.1 0.4 0.5
[1] 5evb.a - 0.2 0 0 2.3 2.3 2.7 0 - - 2.2
0
0.1 0.1 0.2 0.2
[1] 5evd.a - 0.1 0.1 0 2.3 2.4 2.5 0 - - 2.1 0
0.1
0 0.2 0.2
[1] 5evk.a - 0.5 0 0.3 2.0 2.0 2.5 0 - - 2.5 0.7 0.7
0
0.2 0.2
[1] 5hh5.a - 0.5 0.2 0.1 1.9 2.0 2.3 0.1 - - 2.6 0.7 0.7 0
0.1
0.2
[1] 5hh6.a - 0.5 0.2 0.1 1.9 2.2 2.3 0 - - 1.9 0.7 0.7 0 0.1
0.2
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
1sml.a
2aio.a
2fu8.a
2fu9.a
2gfj.a
2gfk.b
2hb9.a
2qdt.a
2qin.b
2qjs.a
5dpx.b
5evb.a
5evd.a
5evk.a
5hh5.a
5hh6.a
[1] 1sml.a
0
.14 .04 .15 .18 .23 .19 .03 .14 .25 .20 .18 .17 .06 .07 .10
[1] 2aio.a .14
0
.11 .03 .23 .18 .27 .12 .04 .17 .18 .06 .05 .09 .10 .07
[1] 2fu8.a .04 .11
0
.11 .20 .23 .17 .02 .12 .22 .19 .14 .13 .03 .04 .07
[1] 2fu9.a .15 .03 .11
0
.24 .19 .28 .13 .01 .18 .20 .04 .06 .09 .11 .08
[1] 2gfj.a .18 .23 .20 .24
0
.05 .09 .20 .24 .09 .26 .27 .26 .17 .18 .18
[1] 2gfk.b .23 .18 .23 .19 .05
0
.12 .23 .18 .06 .31 .23 .22 .21 .21 .21
[1] 2hb9.a .19 .27 .17 .28 .09 .12
0
.17 .29 .13 .29 .32 .29 .19 .17 .21
[1] 2qdt.a .03 .12 .02 .13 .20 .23 .17
0
.14 .24 .21 .16 .15 .05 .05 .08
[1] 2qin.b .14 .04 .12 .01 .24 .18 .29 .14
0
.19 .21 .05 .07 .11 .12 .09
[1] 2qjs.a .25 .17 .22 .18 .09 .06 .13 .24 .19
0
.27 .21 .20 .19 .21 .19
[1] 5dpx.b .20 .18 .19 .20 .26 .31 .29 .21 .21 .27
0
.16 .14 .17 .15 .12
[1] 5evb.a .18 .06 .14 .04 .27 .23 .32 .16 .05 .21 .16
0
.02 .13 .14 .11
[1] 5evd.a .17 .05 .13 .06 .26 .22 .29 .15 .07 .20 .14 .02
0
.12 .12 .09
[1] 5evk.a .06 .09 .03 .09 .17 .21 .19 .05 .11 .19 .17 .13 .12
0
.02 .05
[1] 5hh5.a .07 .10 .04 .11 .18 .21 .17 .05 .12 .21 .15 .14 .12 .02
0
.03
[1] 5hh6.a .10 .07 .07 .08 .18 .21 .21 .08 .09 .19 .12 .11 .09 .05 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1sml.a
2aio.a
2fu8.a
2fu9.a
2gfj.a
2gfk.b
2hb9.a
2qdt.a
2qin.b
2qjs.a
5dpx.b
5evb.a
5evd.a
5evk.a
5hh5.a
5hh6.a
[1] 1sml.a
0
0.3 0.2 0.2 0.4 0.3 0.4 0.1 0.4 0.4 0.4 0.3 0.3 0.2 0.3 0.3
[1] 2aio.a 0.3
0
0.3 0.3 0.5 0.4 0.4 0.3 0.5 0.3 0.5 0.2 0.2 0.3 0.3 0.3
[1] 2fu8.a 0.2 0.3
0
0.2 0.3 0.3 0.4 0.1 0.4 0.4 0.4 0.2 0.2 0.1 0.2 0.2
[1] 2fu9.a 0.2 0.3 0.2
0
0.3 0.3 0.4 0.2 0.4 0.3 0.4 0.2 0.2 0.2 0.3 0.3
[1] 2gfj.a 0.4 0.5 0.3 0.3
0
0.1 0.3 0.4 0.6 0.4 0.5 0.4 0.4 0.4 0.4 0.4
[1] 2gfk.b 0.3 0.4 0.3 0.3 0.1
0
0.3 0.3 0.5 0.3 0.5 0.3 0.3 0.3 0.4 0.4
[1] 2hb9.a 0.4 0.4 0.4 0.4 0.3 0.3
0
0.4 0.6 0.5 0.3 0.4 0.3 0.3 0.3 0.3
[1] 2qdt.a 0.1 0.3 0.1 0.2 0.4 0.3 0.4
0
0.4 0.4 0.4 0.3 0.3 0.2 0.3 0.3
[1] 2qin.b 0.4 0.5 0.4 0.4 0.6 0.5 0.6 0.4
0
0.3 0.5 0.4 0.4 0.4 0.4 0.4
[1] 2qjs.a 0.4 0.3 0.4 0.3 0.4 0.3 0.5 0.4 0.3
0
0.5 0.3 0.3 0.3 0.4 0.4
[1] 5dpx.b 0.4 0.5 0.4 0.4 0.5 0.5 0.3 0.4 0.5 0.5
0
0.4 0.3 0.3 0.2 0.2
[1] 5evb.a 0.3 0.2 0.2 0.2 0.4 0.3 0.4 0.3 0.4 0.3 0.4
0
0.1 0.2 0.2 0.2
[1] 5evd.a 0.3 0.2 0.2 0.2 0.4 0.3 0.3 0.3 0.4 0.3 0.3 0.1
0
0.2 0.2 0.2
[1] 5evk.a 0.2 0.3 0.1 0.2 0.4 0.3 0.3 0.2 0.4 0.3 0.3 0.2 0.2
0
0.2 0.1
[1] 5hh5.a 0.3 0.3 0.2 0.3 0.4 0.4 0.3 0.3 0.4 0.4 0.2 0.2 0.2 0.2
0
0.1
[1] 5hh6.a 0.3 0.3 0.2 0.3 0.4 0.4 0.3 0.3 0.4 0.4 0.2 0.2 0.2 0.1 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1sml.a
2aio.a
2fu8.a
2fu9.a
2gfj.a
2gfk.b
2hb9.a
2qdt.a
2qin.b
2qjs.a
5dpx.b
5evb.a
5evd.a
5evk.a
5hh5.a
5hh6.a
[1] 1sml.a
0
1.0 0.6 0.6 1.1 1.4 1.0 0.2 0.7 0.8 1.0 0.9 1.1 0.8 0.8 0.7
[1] 2aio.a 1.0
0
0.7 0.9 1.2 1.1 1.3 1.0 1.2 0.7 0.9 0.6 0.6 0.7 0.8 0.8
[1] 2fu8.a 0.6 0.7
0
0.6 1.0 1.2 1.1 0.5 0.9 0.7 0.7 0.7 0.9 0.4 0.5 0.5
[1] 2fu9.a 0.6 0.9 0.6
0
1.1 1.3 1.1 0.6 0.8 0.6 0.9 0.6 0.8 0.8 0.6 0.6
[1] 2gfj.a 1.1 1.2 1.0 1.1
0
0.8 0.7 1.1 1.4 0.8 1.2 1.1 1.2 1.1 1.0 1.0
[1] 2gfk.b 1.4 1.1 1.2 1.3 0.8
0
1.0 1.4 1.7 0.7 1.3 1.2 1.0 1.3 1.2 1.2
[1] 2hb9.a 1.0 1.3 1.1 1.1 0.7 1.0
0
1.0 1.3 0.8 1.2 1.2 1.3 1.2 1.1 1.0
[1] 2qdt.a 0.2 1.0 0.5 0.6 1.1 1.4 1.0
0
0.7 0.7 1.0 0.9 1.1 0.8 0.8 0.7
[1] 2qin.b 0.7 1.2 0.9 0.8 1.4 1.7 1.3 0.7
0
0.4 1.2 1.0 1.3 1.1 1.1 1.0
[1] 2qjs.a 0.8 0.7 0.7 0.6 0.8 0.7 0.8 0.7 0.4
0
1.0 0.7 0.7 0.7 0.7 0.7
[1] 5dpx.b 1.0 0.9 0.7 0.9 1.2 1.3 1.2 1.0 1.2 1.0
0
0.8 0.9 0.7 0.8 0.8
[1] 5evb.a 0.9 0.6 0.7 0.6 1.1 1.2 1.2 0.9 1.0 0.7 0.8
0
0.6 0.7 0.5 0.5
[1] 5evd.a 1.1 0.6 0.9 0.8 1.2 1.0 1.3 1.1 1.3 0.7 0.9 0.6
0
1.0 0.8 0.8
[1] 5evk.a 0.8 0.7 0.4 0.8 1.1 1.3 1.2 0.8 1.1 0.7 0.7 0.7 1.0
0
0.5 0.6
[1] 5hh5.a 0.8 0.8 0.5 0.6 1.0 1.2 1.1 0.8 1.1 0.7 0.8 0.5 0.8 0.5
0
0.1
[1] 5hh6.a 0.7 0.8 0.5 0.6 1.0 1.2 1.0 0.7 1.0 0.7 0.8 0.5 0.8 0.6 0.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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