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BLS_STRCL_1_513

Carboxyethyl-arginine beta-lactam-synthase [Asparagine synthetase family]

Composition of the binding site

Protein chains monomer
A1 (BLS_STRCL):247:249, 251:254, 271:273, 280, 326, 330, 333, 346:349, 351, 352, 357, 373, 380, 382, 423, 443:447247:249, 251:254, 271:273, 280, 326, 330, 333, 346:349, 351, 352, 357, 373, 380, 382, 423, 443:447
Metals (Me):Mg

Full PDB list

1jgt, 1m1z, 1mb9, 1mbz, 1mc1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
V
2
4
7
L
2
4
8
S
2
4
9
G
2
5
1
I
2
5
2
D
2
5
3
S
2
5
4
V
2
7
1
S
2
7
2
M
2
7
3
Y
3
2
6
L
3
3
0
L
3
3
3
T
3
4
6
G
3
4
7
Y
3
4
8
G
3
4
9
D
3
5
1
I
3
5
2
M
3
5
7
D
3
7
3
L
3
8
0
E
3
8
2
K
4
2
3
K
4
4
3
L
4
4
4
G
4
4
5
V
4
4
6
[1]1jgt.a apc,cma48 . . . . . . . . . . . . . . . . . . . . . . . . . . - - Mg
[1]1m1z.a none . . . . . . . . . . . . . . . . . . . . . . . . . - - -
[1]1mb9.a amp,atp54 . . . . . . . . . . . . . . . . . . . . . . . . . - - - Mg
[1]1mb9.b atp31 . . . . . . . . . . . . . . . . . . . . . . . . . . . - Mg
[1]1mbz.a iot38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]1mc1.a amp,pcx39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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
V
2
4
7
L
2
4
8
S
2
4
9
G
2
5
1
I
2
5
2
D
2
5
3
S
2
5
4
V
2
7
1
S
2
7
2
M
2
7
3
E
2
8
0
Y
3
2
6
L
3
3
0
L
3
3
3
T
3
4
6
G
3
4
7
Y
3
4
8
G
3
4
9
D
3
5
1
I
3
5
2
M
3
5
7
D
3
7
3
L
3
8
0
E
3
8
2
K
4
2
3
K
4
4
3
L
4
4
4
G
4
4
5
V
4
4
6
H
4
4
7
[1]1jgt.a . . . . . . . . . . . . . . . . . . . . . . . . . . . - - - Mg
[1]1m1z.a . . . . . . . . . . . * . . . . . . . . . . . . . . - - - -
[1]1mb9.a . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - Mg
[1]1mb9.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - Mg
[1]1mbz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . Mg
[1]1mc1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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
1jgt.a:apc,cma
1m1z.a is apo
1mb9.a:amp,atp
1mb9.b:atp
1mbz.a:iot
1mc1.a:amp,pcx
[1] 1jgt.a
0.2
- 0.4 0.2 0.2 0.2
[1] 1m1z.a 2.5
-
1.9 1.1 1.3 1.0
[1] 1mb9.a 0.6 -
0.1
0.3 0.3 0.3
[1] 1mb9.b 0.6 - 0.2
0.1
0.5 0.4
[1] 1mbz.a 1.3 - 1.3 0.8
0
0.3
[1] 1mc1.a 0.7 - 0.9 0.6 0.5
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
1jgt.a
1m1z.a
1mb9.a
1mb9.b
1mbz.a
1mc1.a
[1] 1jgt.a
0
.09 .03 .03 .06 .03
[1] 1m1z.a .09
0
.08 .10 .12 .09
[1] 1mb9.a .03 .08
0
.03 .06 .04
[1] 1mb9.b .03 .10 .03
0
.07 .05
[1] 1mbz.a .06 .12 .06 .07
0
.03
[1] 1mc1.a .03 .09 .04 .05 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
1jgt.a
1m1z.a
1mb9.a
1mb9.b
1mbz.a
1mc1.a
[1] 1jgt.a
0
0.5 0.4 0.6 1.6 1.4
[1] 1m1z.a 0.5
0
0.5 0.5 0.9 0.6
[1] 1mb9.a 0.4 0.5
0
0.3 0.9 0.4
[1] 1mb9.b 0.6 0.5 0.3
0
2.2 2.1
[1] 1mbz.a 1.6 0.9 0.9 2.2
0
0.7
[1] 1mc1.a 1.4 0.6 0.4 2.1 0.7
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
1jgt.a
1m1z.a
1mb9.a
1mb9.b
1mbz.a
1mc1.a
[1] 1jgt.a
0
1.6 1.2 1.5 1.6 1.4
[1] 1m1z.a 1.6
0
1.2 1.4 1.7 1.6
[1] 1mb9.a 1.2 1.2
0
0.9 1.3 1.2
[1] 1mb9.b 1.5 1.4 0.9
0
2.4 2.4
[1] 1mbz.a 1.6 1.7 1.3 2.4
0
0.9
[1] 1mc1.a 1.4 1.6 1.2 2.4 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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