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CARA_PECCC_1_503

Carbapenam-3-carboxylate synthase

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CARA_PECCC):D: Asparagine synthetase (244:246, 248:251, 268:270, 327, 343:345, 348, 421, 443)
444:446
244:246, 248:251, 268:270, 327, 343:345, 348, 421, 443:446
Cofactors (cF):ssc
Metals (Me):Mg

Full PDB list

1q15, 1q19

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
P
2
4
4
L
2
4
5
S
2
4
6
G
2
4
8
L
2
4
9
D
2
5
0
S
2
5
1
Y
2
6
8
S
2
6
9
I
2
7
0
L
3
2
7
T
3
4
3
G
3
4
4
Y
3
4
5
D
3
4
8
K
4
2
1
K
4
4
3
I
4
4
4
G
4
4
5
I
4
4
6
[1]1q15.b none . . . . . . . . . . . . . . . . - - - -
[1]1q19.a apc31 . . . . . . . . . . . . . . . . . . . . ssc 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 cF Me
P
2
4
4
L
2
4
5
S
2
4
6
G
2
4
8
L
2
4
9
D
2
5
0
S
2
5
1
Y
2
6
8
S
2
6
9
I
2
7
0
L
3
2
7
T
3
4
3
G
3
4
4
Y
3
4
5
D
3
4
8
K
4
2
1
K
4
4
3
I
4
4
4
G
4
4
5
I
4
4
6
[1]1q15.b . . . . . . . . . . . . . . . . - - - -
[1]1q19.a . . . . . . . . . . . . . . . . . . . . ssc 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
1q15.b is apo
1q19.a:apc
[1] 1q15.b
-
1.1
[1] 1q19.a -
0.1
[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
1q15.b
1q19.a
[1] 1q15.b
0
.05
[1] 1q19.a .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1q15.b
1q19.a
[1] 1q15.b
0
0.4
[1] 1q19.a 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1q15.b
1q19.a
[1] 1q15.b
0
0.6
[1] 1q19.a 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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