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CARC_PECCC_1_273

(5R)-carbapenem-3-carboxylate synthase [TfdA dioxygenase family]

Composition of the binding site

Protein chains monomer
A1 (CARC_PECCC):92, 101:107, 164, 165, 191, 202, 267, 26992, 101:107, 164, 165, 191, 202, 267, 269
Metals (Me):Fe

Full PDB list

1nx4, 1nx8, 4oj8 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
V
9
2
H
1
0
1
A
1
0
2
D
1
0
3
G
1
0
4
L
1
0
6
L
1
0
7
Y
1
6
4
Y
1
6
5
Y
1
9
1
W
2
0
2
R
2
6
7
Q
2
6
9
[1]1nx8.a none . . . . . . . - - . . . . Fe
[1]1nx8.c n7p11 . . . . . . . - - . . . . Fe
[1]4oj8.b 2tq11 . . . . . . . . . . . . . Fe

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
9
2
H
1
0
1
A
1
0
2
D
1
0
3
G
1
0
4
G
1
0
5
L
1
0
6
L
1
0
7
Y
1
6
4
Y
1
6
5
Y
1
9
1
W
2
0
2
R
2
6
7
Q
2
6
9
[1]1nx8.a . . . . . . . . - - . . . . Fe
[1]1nx8.c . . . . . . . . - - . . . . Fe
[1]4oj8.b . . . . . . . . . . . . . . Fe

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
1nx8.a is apo
1nx8.c:n7p
4oj8.b:2tq
[1] 1nx8.a
-
0.3 0
[1] 1nx8.c -
0.1
0
[1] 4oj8.b - 0.6
0
[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
1nx8.a
1nx8.c
4oj8.b
[1] 1nx8.a
0
.01 .04
[1] 1nx8.c .01
0
.04
[1] 4oj8.b .04 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1nx8.a
1nx8.c
4oj8.b
[1] 1nx8.a
0
0.5 0.6
[1] 1nx8.c 0.5
0
0.4
[1] 4oj8.b 0.6 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1nx8.a
1nx8.c
4oj8.b
[1] 1nx8.a
0
0.4 0.6
[1] 1nx8.c 0.4
0
0.4
[1] 4oj8.b 0.6 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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