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BLAC_STAAU_23_244

Beta-lactamase [Class-A beta-lactamase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BLAC_STAAU):R: Substrate binding (225:227)
62, 63, 66, 96, 121, 123, 157, 158, 161, 207, 228:230, 235
62, 63, 66, 96, 121, 123, 157, 158, 161, 207, 225:230, 235

Full PDB list

1blc, 1blh, 1blp, 1dja, 1djb, 1djc, 1ghi, 1ghm, 1ghp, 1kge, 1kgf, 1kgg, 1ome, 1pio, 3blm (redundant Pocketome entry); 1alq (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
6
2
S
6
3
K
6
6
Y
9
6
S
1
2
1
N
1
2
3
I
1
5
8
N
1
6
1
S
2
0
7
K
2
2
5
S
2
2
6
G
2
2
7
Q
2
2
8
A
2
2
9
I
2
3
0
R
2
3
5
[1]1blc.a cem,tem25 . * . . . . . . . . . . . . . .
[1]1blh.a fos15 . * . . . . . . . . . . . . . .
[1]1dja.a none . . H . . . . . . . . . . . . .
[1]1djb.a none . A . . . . . . . . . . . . . .
[1]1ghi.a none . . . . . . . Q . . . . . . . .
[1]1ghm.a ced22 . * . . . . . Q . . . . . . . .
[1]1ghp.a pnm23 . * . . . . . Q . . . . . . . .
[1]1kge.a none . . . . . . . M . . . . . . . .
[1]1kgf.a none . . . . . . . Q . . . . . . . .
[1]1kgg.a none . . . . . . . D . . . . . . . .
[1]1pio.a none . . . . . . . . . . . . . S - .
[1]3blm.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
A
6
2
S
6
3
K
6
6
Y
9
6
S
1
2
1
N
1
2
3
E
1
5
7
I
1
5
8
N
1
6
1
S
2
0
7
K
2
2
5
S
2
2
6
G
2
2
7
Q
2
2
8
A
2
2
9
I
2
3
0
R
2
3
5
[1]1blc.a . * . . . . . . . . . . . . . . .
[1]1blh.a . * . . . . . . . . . . . . . . .
[1]1dja.a . . H . . . . . . . . . . . . . .
[1]1djb.a . A . . . . . . . . . . . . . . .
[1]1ghi.a . * . . . . D . Q . . . . . . . .
[1]1ghm.a . * . . . . D . Q . . . . . . . .
[1]1ghp.a . * . . . . D . Q . . . . . . . .
[1]1kge.a . . . . . . . . M . . . . . . . .
[1]1kgf.a . . . . . . . . Q . . . . . . . .
[1]1kgg.a . * . . . . Q . D . . . . . . . .
[1]1pio.a . * . . . . . . . . . . . . S - .
[1]3blm.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
1blc.a:cem,tem
1blh.a:fos
1dja.a is apo
1djb.a is apo
1ghi.a is apo
1ghm.a:ced
1ghp.a:pnm
1kge.a is apo
1kgf.a is apo
1kgg.a is apo
1pio.a is apo
3blm.a is apo
[1] 1blc.a
1.2
0.9 - - - 1.0 0.6 - - - - -
[1] 1blh.a 1.0
0.7
- - - 0.4 0.4 - - - - -
[1] 1dja.a 0.9 0.6
-
- - 0.4 0.5 - - - - -
[1] 1djb.a 0.6 0.3 -
-
- 0.3 0.1 - - - - -
[1] 1ghi.a 1.7 1.3 - -
-
1.1 1.3 - - - - -
[1] 1ghm.a 1.3 1.0 - - -
0.8
0.9 - - - - -
[1] 1ghp.a 1.6 1.1 - - - 0.8
0.8
- - - - -
[1] 1kge.a 1.5 1.2 - - - 1.0 1.2
-
- - - -
[1] 1kgf.a 0.9 0.9 - - - 0.6 0.8 -
-
- - -
[1] 1kgg.a 1.7 1.1 - - - 1.1 1.2 - -
-
- -
[1] 1pio.a 1.3 0.8 - - - 0.9 1.0 - - -
-
-
[1] 3blm.a 0.8 0.6 - - - 0.6 0.4 - - - -
-
[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
1blc.a
1blh.a
1dja.a
1djb.a
1ghi.a
1ghm.a
1ghp.a
1kge.a
1kgf.a
1kgg.a
1pio.a
3blm.a
[1] 1blc.a
0
.04 .03 .05 .07 .03 .04 .09 .05 .04 .03 .03
[1] 1blh.a .04
0
.02 .03 .05 .03 .03 .05 .03 .05 .05 .02
[1] 1dja.a .03 .02
0
.03 .06 .03 .04 .06 .03 .05 .04 .01
[1] 1djb.a .05 .03 .03
0
.07 .05 .06 .07 .03 .06 .06 .02
[1] 1ghi.a .07 .05 .06 .07
0
.05 .05 .02 .04 .06 .06 .06
[1] 1ghm.a .03 .03 .03 .05 .05
0
.02 .07 .04 .04 .04 .04
[1] 1ghp.a .04 .03 .04 .06 .05 .02
0
.07 .05 .05 .05 .05
[1] 1kge.a .09 .05 .06 .07 .02 .07 .07
0
.04 .08 .07 .06
[1] 1kgf.a .05 .03 .03 .03 .04 .04 .05 .04
0
.05 .05 .02
[1] 1kgg.a .04 .05 .05 .06 .06 .04 .05 .08 .05
0
.02 .05
[1] 1pio.a .03 .05 .04 .06 .06 .04 .05 .07 .05 .02
0
.04
[1] 3blm.a .03 .02 .01 .02 .06 .04 .05 .06 .02 .05 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1blc.a
1blh.a
1dja.a
1djb.a
1ghi.a
1ghm.a
1ghp.a
1kge.a
1kgf.a
1kgg.a
1pio.a
3blm.a
[1] 1blc.a
0
0.4 0.5 0.5 0.5 0.4 0.5 0.4 0.5 0.6 0.8 0.5
[1] 1blh.a 0.4
0
0.3 0.2 0.2 0.2 0.3 0.2 0.2 0.5 0.7 0.2
[1] 1dja.a 0.5 0.3
0
0.2 0.3 0.3 0.3 0.3 0.3 0.5 0.7 0.2
[1] 1djb.a 0.5 0.2 0.2
0
0.2 0.3 0.3 0.2 0.2 0.4 0.7 0.1
[1] 1ghi.a 0.5 0.2 0.3 0.2
0
0.3 0.3 0.2 0.2 0.4 0.7 0.2
[1] 1ghm.a 0.4 0.2 0.3 0.3 0.3
0
0.2 0.3 0.3 0.5 0.8 0.3
[1] 1ghp.a 0.5 0.3 0.3 0.3 0.3 0.2
0
0.3 0.3 0.6 0.8 0.3
[1] 1kge.a 0.4 0.2 0.3 0.2 0.2 0.3 0.3
0
0.2 0.4 0.7 0.1
[1] 1kgf.a 0.5 0.2 0.3 0.2 0.2 0.3 0.3 0.2
0
0.4 0.8 0.2
[1] 1kgg.a 0.6 0.5 0.5 0.4 0.4 0.5 0.6 0.4 0.4
0
0.8 0.4
[1] 1pio.a 0.8 0.7 0.7 0.7 0.7 0.8 0.8 0.7 0.8 0.8
0
0.7
[1] 3blm.a 0.5 0.2 0.2 0.1 0.2 0.3 0.3 0.1 0.2 0.4 0.7
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

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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
1blc.a
1blh.a
1dja.a
1djb.a
1ghi.a
1ghm.a
1ghp.a
1kge.a
1kgf.a
1kgg.a
1pio.a
3blm.a
[1] 1blc.a
0
0.8 1.6 1.6 1.6 0.8 0.6 1.6 1.5 1.7 1.2 1.6
[1] 1blh.a 0.8
0
1.4 1.4 1.4 0.8 0.7 1.4 1.2 1.5 1.0 1.4
[1] 1dja.a 1.6 1.4
0
0.3 0.7 1.4 1.4 0.4 0.5 0.7 1.3 0.7
[1] 1djb.a 1.6 1.4 0.3
0
0.6 1.4 1.4 0.3 0.4 0.7 1.3 0.7
[1] 1ghi.a 1.6 1.4 0.7 0.6
0
1.3 1.4 0.6 0.7 0.9 1.4 0.3
[1] 1ghm.a 0.8 0.8 1.4 1.4 1.3
0
0.5 1.4 1.3 1.4 0.9 1.3
[1] 1ghp.a 0.6 0.7 1.4 1.4 1.4 0.5
0
1.4 1.3 1.6 1.1 1.4
[1] 1kge.a 1.6 1.4 0.4 0.3 0.6 1.4 1.4
0
0.3 0.6 1.3 0.7
[1] 1kgf.a 1.5 1.2 0.5 0.4 0.7 1.3 1.3 0.3
0
0.7 1.2 0.7
[1] 1kgg.a 1.7 1.5 0.7 0.7 0.9 1.4 1.6 0.6 0.7
0
1.3 0.9
[1] 1pio.a 1.2 1.0 1.3 1.3 1.4 0.9 1.1 1.3 1.2 1.3
0
1.4
[1] 3blm.a 1.6 1.4 0.7 0.7 0.3 1.3 1.4 0.7 0.7 0.9 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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