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BLAB_SERMA_18_245

Metallo-beta-lactamase type 2 [Metallo-beta-lactamase superfamily. Class-B beta-lactamase family]

Composition of the binding site

Protein chains monomer
A1 (BLAB_SERMA):39:41, 43:46, 49:51, 69, 95, 97:99, 157, 176, 179, 181:185, 215, 216, 238:24139:41, 43:46, 49:51, 69, 95, 97:99, 157, 176, 179, 181:185, 215, 216, 238:241
Metals (Me):Fe/Zn

Full PDB list

1dd6, 1ddk, 1jje, 1jjt, 1vgn, 1wuo, 1wup, 2doo, 3wxc, 4c1f, 4c1g, 4f6h, 4f6z, 4uam, 5ev6, 5ev8, 5ewa, 5hh4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
E
4
1
V
4
3
W
4
6
V
4
9
K
5
1
F
6
9
H
9
5
H
9
7
S
9
8
D
9
9
H
1
5
7
C
1
7
6
K
1
7
9
Y
1
8
1
G
1
8
2
L
1
8
3
G
1
8
4
N
1
8
5
H
2
1
5
[1]1dd6.a mci29 . . . . . . . . . . . . . . . . . . . Zn
[1]1jje.a bys25 . . . . . . . . . . . . . . . . . . . Zn
[1]1jjt.a bds28 . . . . . . . . . . . . . . . . . . . Zn
[1]1vgn.b ops10 . . . . . . . . . . . . * . . . . . . Zn
[1]3wxc.a c9319 . . . . . . . . . . . . . . . . . . . Zn
[1]4c1f.a x8z14 . . . . . . . . . . . . . . . . . . . Zn
[1]4c1g.a mco14 . . . . . . . . . . . . . . . . . . . Zn
[1]5ev6.b none . . . . . . . . . . . . . . . . . . . Zn
[1]5ev8.a 3r913 . . . . . . . . . . . . . . . . . . . Zn
[1]5ewa.b 9bz15 . . . . . . . . . . . . . . . . . . . Zn
[1]5hh4.a 60m14 . . . . . . . . . . . . . . . . . . . Zn
[2]1wuo.c none . . . . . . . . . A . * . . . . . . . Zn
[2]1wup.b none . . . . . . . . . E . . . . . . . . . Zn
[2]2doo.b c4h27 . . . . . . . . . . . . . . . . . . . Zn
[2]4f6h.a none . . . . . . . . . . . G . . . . . . . Zn
[2]4f6z.a none . . . . . . . . . . . G . . . . . . . Zn
[2]4uam.a none . . . . . . . . . . . * . . . . . . . Fe,Zn
[2]5ev8.c 3r9,3r926 . . . . . . . . . . . . . . . . . . . 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
S
3
9
F
4
0
E
4
1
V
4
3
N
4
4
G
4
5
W
4
6
V
4
9
P
5
0
K
5
1
F
6
9
H
9
5
H
9
7
S
9
8
D
9
9
H
1
5
7
C
1
7
6
K
1
7
9
Y
1
8
1
G
1
8
2
L
1
8
3
G
1
8
4
N
1
8
5
H
2
1
5
S
2
1
6
S
2
3
8
K
2
3
9
K
2
4
0
P
2
4
1
[1]1dd6.a . . . . . . * . . . . . . . . . . . . . . . . . . - - - - Zn
[1]1jje.a . . . . . . * . . . * . . . . . . . . . . . . . . . . . - Zn
[1]1jjt.a . . . . . . * . . . * . . . . . . . . . . . . . . . . . - Zn
[1]1vgn.b . . . . . . * . . . * . . . . . . * . . . . . . . . . - - Zn
[1]3wxc.a . . . . . . * . . . * . . . . . . . . . . . . . . . - - - Zn
[1]4c1f.a . . . . . . * . . . * . . . . . . . . . . . . . . . . - - Zn
[1]4c1g.a . . . . . . * . . . * . . . . . . . . . . . . . . . . - - Zn
[1]5ev6.b . . . . . . * . . . * . . . . . . . . . . . . . . . . - - Zn
[1]5ev8.a . . . . . . * . . . * . . . * . . . . . . . . . . . . - - Zn
[1]5ewa.b . . . . . . * . . . * . . . . . . . . . . . . . . . . - - Zn
[1]5hh4.a . . . . . . * . . . * . . . . . . . . . . . . . . . - - - Zn
[2]1wuo.c . . * . . . . . . . * . . . A . * . . . . . . . . . . - - Zn
[2]1wup.b . . . . . . . * . . * . . . E . . * . . . . . . . - - - - Zn
[2]2doo.b . . . . . . . . . . * . . . . . . . . . . . . . . - - - - Zn
[2]4f6h.a . . * . . . . . . . * . . . . . G . . . . . . . . . H P Q Zn
[2]4f6z.a . . . . . . . . . . * . . . . . G . . . . . . . . H P Q F Zn
[2]4uam.a . . . . . . . . . . * . . . . . * . . . . . . . . . . . - Fe,Zn
[2]5ev8.c . . * . . . . . . . . . . . . . . . . . . . . . . . . . . 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
1dd6.a:mci
1jje.a:bys
1jjt.a:bds
1vgn.b:ops
3wxc.a:c93
4c1f.a:x8z
4c1g.a:mco
5ev6.b is apo
5ev8.a:3r9
5ewa.b:9bz
5hh4.a:60m
1wuo.c is apo
1wup.b is apo
2doo.b:c4h
4f6h.a is apo
4f6z.a is apo
4uam.a is apo
5ev8.c:3r9
[1] 1dd6.a
0
0.4 0.8 0.1 0.1 0 0 - 0.1 0.4 0 - - 0 - - - 4.7
[1] 1jje.a 3.7
0
0.8 0.2 0 0.1 0.2 - 0.5 1.4 0 - - 0.2 - - - 4.2
[1] 1jjt.a 3.0 0
0
0.2 0 0.2 0.1 - 0.5 1.3 0.2 - - 0.1 - - - 3.3
[1] 1vgn.b 3.3 1.0 1.6
0.6
0.5 0.6 0.7 - 0.4 1.6 0.2 - - 0.3 - - - 5.9
[1] 3wxc.a 4.1 1.4 1.0 0.2
0
0.7 0.5 - 0.1 1.9 0 - - 0.4 - - - 4.7
[1] 4c1f.a 3.3 0.2 0.5 0 0.1
0.1
0 - 0.1 0.2 0 - - 0.1 - - - 5.0
[1] 4c1g.a 3.0 0.5 0.7 0.4 0.4 0.1
0.1
- 0.1 0.4 0 - - 0.2 - - - 5.2
[1] 5ev6.b 3.5 0.8 0.9 0.2 0.1 0.3 0.1
-
0.5 1.3 0.1 - - 0.1 - - - 5.5
[1] 5ev8.a 3.9 2.0 1.4 0.2 1.1 0.8 0.2 -
0.1
0.9 0.9 - - 0.4 - - - 4.0
[1] 5ewa.b 3.0 0.5 0.5 0.1 0.1 0.1 0.1 - 0.4
0.3
0.1 - - 0.1 - - - 5.2
[1] 5hh4.a 3.8 1.0 1.4 0.2 0 0.3 0.3 - 0.4 1.3
0
- - 0.2 - - - 5.2
[2] 1wuo.c 3.5 0.5 2.0 0.4 0.5 0.8 0.4 - 0.5 0.4 0.5
-
- 0.4 - - - 0.5
[2] 1wup.b 3.4 1.3 1.6 2.1 1.5 1.8 1.5 - 1.9 2.6 0.4 -
-
1.0 - - - 2.2
[2] 2doo.b 2.1 0.2 0.4 0.1 0.1 0 0 - 0.1 0.1 0 - -
0
- - - 1.0
[2] 4f6h.a 3.2 0.6 1.4 0.1 0 0.3 0.4 - 0.2 0.5 0 - - 1.1
-
- - 1.5
[2] 4f6z.a 3.5 0.7 1.5 0.3 0.2 0.5 0.5 - 0.3 0.8 0 - - 1.3 -
-
- 1.9
[2] 4uam.a 2.2 0.1 1.1 0.5 0.2 0.3 0.2 - 0.6 0.8 0 - - 0.1 - -
-
1.0
[2] 5ev8.c 2.4 0 1.4 0.1 0.2 0.3 0 - 0.1 0.5 0.2 - - 0 - - -
0
[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
1dd6.a
1jje.a
1jjt.a
1vgn.b
3wxc.a
4c1f.a
4c1g.a
5ev6.b
5ev8.a
5ewa.b
5hh4.a
1wuo.c
1wup.b
2doo.b
4f6h.a
4f6z.a
4uam.a
5ev8.c
[1] 1dd6.a
0
.19 .18 .14 .14 .12 .12 .14 .14 .13 .14 .30 .30 .20 .27 .28 .24 .23
[1] 1jje.a .19
0
.06 .14 .09 .13 .14 .09 .11 .13 .10 .30 .25 .20 .31 .29 .23 .30
[1] 1jjt.a .18 .06
0
.16 .09 .13 .14 .12 .11 .13 .13 .25 .21 .15 .27 .24 .19 .25
[1] 1vgn.b .14 .14 .16
0
.11 .10 .07 .08 .14 .09 .07 .33 .30 .23 .36 .32 .28 .36
[1] 3wxc.a .14 .09 .09 .11
0
.07 .09 .09 .08 .09 .06 .31 .25 .21 .32 .31 .26 .33
[1] 4c1f.a .12 .13 .13 .10 .07
0
.03 .09 .08 .05 .05 .31 .30 .19 .31 .30 .26 .34
[1] 4c1g.a .12 .14 .14 .07 .09 .03
0
.08 .09 .04 .06 .30 .29 .19 .32 .30 .27 .34
[1] 5ev6.b .14 .09 .12 .08 .09 .09 .08
0
.11 .07 .04 .34 .30 .23 .36 .31 .27 .34
[1] 5ev8.a .14 .11 .11 .14 .08 .08 .09 .11
0
.10 .10 .31 .24 .20 .32 .29 .24 .32
[1] 5ewa.b .13 .13 .13 .09 .09 .05 .04 .07 .10
0
.07 .29 .30 .20 .31 .30 .28 .33
[1] 5hh4.a .14 .10 .13 .07 .06 .05 .06 .04 .10 .07
0
.34 .31 .22 .35 .32 .27 .36
[2] 1wuo.c .30 .30 .25 .33 .31 .31 .30 .34 .31 .29 .34
0
.19 .15 .13 .15 .10 .10
[2] 1wup.b .30 .25 .21 .30 .25 .30 .29 .30 .24 .30 .31 .19
0
.18 .20 .19 .15 .19
[2] 2doo.b .20 .20 .15 .23 .21 .19 .19 .23 .20 .20 .22 .15 .18
0
.14 .13 .09 .17
[2] 4f6h.a .27 .31 .27 .36 .32 .31 .32 .36 .32 .31 .35 .13 .20 .14
0
.13 .11 .11
[2] 4f6z.a .28 .29 .24 .32 .31 .30 .30 .31 .29 .30 .32 .15 .19 .13 .13
0
.10 .15
[2] 4uam.a .24 .23 .19 .28 .26 .26 .27 .27 .24 .28 .27 .10 .15 .09 .11 .10
0
.12
[2] 5ev8.c .23 .30 .25 .36 .33 .34 .34 .34 .32 .33 .36 .10 .19 .17 .11 .15 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
1dd6.a
1jje.a
1jjt.a
1vgn.b
3wxc.a
4c1f.a
4c1g.a
5ev6.b
5ev8.a
5ewa.b
5hh4.a
1wuo.c
1wup.b
2doo.b
4f6h.a
4f6z.a
4uam.a
5ev8.c
[1] 1dd6.a
0
1.6 1.4 1.4 1.4 1.6 1.5 0.9 1.4 1.0 1.3 1.3 1.5 1.0 2.4 2.1 1.2 1.0
[1] 1jje.a 1.6
0
0.4 0.8 0.7 0.7 0.7 0.9 0.7 0.9 0.7 1.4 0.8 1.6 6.5 7.2 1.2 1.7
[1] 1jjt.a 1.4 0.4
0
0.8 0.6 0.7 0.7 0.8 0.6 0.7 0.7 1.2 0.8 1.4 6.5 7.2 1.1 1.6
[1] 1vgn.b 1.4 0.8 0.8
0
0.6 0.7 0.6 0.7 0.7 0.8 0.5 1.4 0.9 1.6 5.1 6.3 1.2 1.7
[1] 3wxc.a 1.4 0.7 0.6 0.6
0
0.6 0.6 0.7 0.4 0.7 0.5 1.3 0.8 1.5 2.3 4.3 1.0 1.6
[1] 4c1f.a 1.6 0.7 0.7 0.7 0.6
0
0.3 0.9 0.5 0.8 0.6 1.5 0.8 1.7 5.0 6.2 1.2 1.9
[1] 4c1g.a 1.5 0.7 0.7 0.6 0.6 0.3
0
0.8 0.5 0.8 0.6 1.5 0.8 1.7 5.0 6.2 1.2 1.8
[1] 5ev6.b 0.9 0.9 0.8 0.7 0.7 0.9 0.8
0
0.8 0.6 0.7 1.2 0.9 1.2 4.9 6.1 1.1 1.3
[1] 5ev8.a 1.4 0.7 0.6 0.7 0.4 0.5 0.5 0.8
0
0.6 0.5 1.3 0.8 1.5 4.8 6.1 1.1 1.6
[1] 5ewa.b 1.0 0.9 0.7 0.8 0.7 0.8 0.8 0.6 0.6
0
0.7 1.0 0.9 1.1 4.8 6.1 0.8 1.2
[1] 5hh4.a 1.3 0.7 0.7 0.5 0.5 0.6 0.6 0.7 0.5 0.7
0
1.3 0.8 1.5 2.4 4.5 1.1 1.7
[2] 1wuo.c 1.3 1.4 1.2 1.4 1.3 1.5 1.5 1.2 1.3 1.0 1.3
0
1.3 0.7 4.7 6.1 0.6 0.9
[2] 1wup.b 1.5 0.8 0.8 0.9 0.8 0.8 0.8 0.9 0.8 0.9 0.8 1.3
0
1.5 2.2 1.8 1.0 1.6
[2] 2doo.b 1.0 1.6 1.4 1.6 1.5 1.7 1.7 1.2 1.5 1.1 1.5 0.7 1.5
0
1.8 1.7 0.8 0.5
[2] 4f6h.a 2.4 6.5 6.5 5.1 2.3 5.0 5.0 4.9 4.8 4.8 2.4 4.7 2.2 1.8
0
4.0 6.5 7.3
[2] 4f6z.a 2.1 7.2 7.2 6.3 4.3 6.2 6.2 6.1 6.1 6.1 4.5 6.1 1.8 1.7 4.0
0
7.4 8.2
[2] 4uam.a 1.2 1.2 1.1 1.2 1.0 1.2 1.2 1.1 1.1 0.8 1.1 0.6 1.0 0.8 6.5 7.4
0
1.0
[2] 5ev8.c 1.0 1.7 1.6 1.7 1.6 1.9 1.8 1.3 1.6 1.2 1.7 0.9 1.6 0.5 7.3 8.2 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
1dd6.a
1jje.a
1jjt.a
1vgn.b
3wxc.a
4c1f.a
4c1g.a
5ev6.b
5ev8.a
5ewa.b
5hh4.a
1wuo.c
1wup.b
2doo.b
4f6h.a
4f6z.a
4uam.a
5ev8.c
[1] 1dd6.a
0
1.9 1.9 1.6 1.6 1.7 1.7 1.3 1.6 1.3 1.5 2.5 2.1 1.6 2.7 2.6 1.6 1.5
[1] 1jje.a 1.9
0
0.9 1.2 1.1 1.2 1.2 1.3 1.1 1.4 1.2 2.7 2.0 2.1 6.4 6.9 1.8 2.7
[1] 1jjt.a 1.9 0.9
0
1.3 1.1 1.3 1.3 1.3 1.2 1.3 1.2 2.7 2.1 2.0 6.4 6.9 1.9 2.6
[1] 1vgn.b 1.6 1.2 1.3
0
0.7 1.1 1.0 1.0 1.1 1.1 0.9 2.6 1.9 1.8 4.9 6.0 1.6 2.3
[1] 3wxc.a 1.6 1.1 1.1 0.7
0
0.9 0.9 1.0 0.7 1.0 0.8 2.5 1.9 1.8 2.6 4.0 1.4 2.2
[1] 4c1f.a 1.7 1.2 1.3 1.1 0.9
0
0.6 1.1 0.7 1.0 0.9 2.7 2.0 2.1 4.8 6.0 1.6 2.4
[1] 4c1g.a 1.7 1.2 1.3 1.0 0.9 0.6
0
1.0 0.8 1.0 0.8 2.7 1.9 2.0 4.9 6.0 1.6 2.4
[1] 5ev6.b 1.3 1.3 1.3 1.0 1.0 1.1 1.0
0
1.0 0.8 0.9 2.5 1.8 1.6 4.8 5.8 1.5 2.0
[1] 5ev8.a 1.6 1.1 1.2 1.1 0.7 0.7 0.8 1.0
0
0.9 0.8 2.5 1.9 1.9 4.7 5.8 1.5 2.2
[1] 5ewa.b 1.3 1.4 1.3 1.1 1.0 1.0 1.0 0.8 0.9
0
0.9 2.3 1.8 1.6 4.6 5.8 1.3 1.9
[1] 5hh4.a 1.5 1.2 1.2 0.9 0.8 0.9 0.8 0.9 0.8 0.9
0
2.6 1.8 1.8 2.7 4.2 1.5 2.3
[2] 1wuo.c 2.5 2.7 2.7 2.6 2.5 2.7 2.7 2.5 2.5 2.3 2.6
0
2.1 1.7 4.3 5.7 1.7 2.0
[2] 1wup.b 2.1 2.0 2.1 1.9 1.9 2.0 1.9 1.8 1.9 1.8 1.8 2.1
0
1.8 2.4 2.2 1.6 2.1
[2] 2doo.b 1.6 2.1 2.0 1.8 1.8 2.1 2.0 1.6 1.9 1.6 1.8 1.7 1.8
0
2.0 2.0 1.3 1.6
[2] 4f6h.a 2.7 6.4 6.4 4.9 2.6 4.8 4.9 4.8 4.7 4.6 2.7 4.3 2.4 2.0
0
3.5 5.7 6.9
[2] 4f6z.a 2.6 6.9 6.9 6.0 4.0 6.0 6.0 5.8 5.8 5.8 4.2 5.7 2.2 2.0 3.5
0
6.5 7.5
[2] 4uam.a 1.6 1.8 1.9 1.6 1.4 1.6 1.6 1.5 1.5 1.3 1.5 1.7 1.6 1.3 5.7 6.5
0
1.5
[2] 5ev8.c 1.5 2.7 2.6 2.3 2.2 2.4 2.4 2.0 2.2 1.9 2.3 2.0 2.1 1.6 6.9 7.5 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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