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CPT_STRVP_1_178

Chloramphenicol 3-O phosphotransferase

Composition of the binding site

Protein chains monomer
A1 (CPT_STRVP):11:13, 16, 17, 36, 37, 40, 54, 56, 62, 64, 92, 94, 96, 136, 140, 14411:13, 16, 17, 36, 37, 40, 54, 56, 62, 64, 92, 94, 96, 136, 140, 144

Full PDB list

1grq, 1grr, 1qhn, 1qhs, 1qhx, 1qhy

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
1
1
S
1
2
K
1
6
S
1
7
V
3
6
D
3
7
I
4
0
I
5
4
F
5
6
V
6
2
I
6
4
D
9
2
V
9
4
L
9
6
R
1
3
6
M
1
4
0
Q
1
4
4
[1]1grq.a clk18 . . . . . . . . . . . . . . . . .
[1]1grr.a clc18 . . . . . . . . . . . . . . . . .
[1]1qhn.a none . . . . . . . . . . . . . . . * .
[1]1qhs.a clm20 . . . . . . . . . . . . . . . . .
[1]1qhx.a mg1 . . . . . . . . . . . . . . . . .
[1]1qhy.a clm,mg21 . . . . . . . . . . . . . . . . .

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
G
1
1
S
1
2
S
1
3
K
1
6
S
1
7
V
3
6
D
3
7
I
4
0
I
5
4
F
5
6
V
6
2
I
6
4
D
9
2
V
9
4
L
9
6
R
1
3
6
M
1
4
0
Q
1
4
4
[1]1grq.a . . . . . . . . . . . . . . . . . .
[1]1grr.a . . . . . . . . . . . . . . . . . .
[1]1qhn.a . * . . . . . . . . . . . . . . * .
[1]1qhs.a . . . . . . . . . . . . . . . . . .
[1]1qhx.a . . . . . . . . . . . . . . . . . .
[1]1qhy.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
1grq.a:clk
1grr.a:clc
1qhn.a is apo
1qhs.a:clm
1qhx.a:mg
1qhy.a:clm,mg
[1] 1grq.a
0.5
0.1 - 0.1 0 0.1
[1] 1grr.a 1.1
0
- 0.2 0 0
[1] 1qhn.a 1.3 0.1
-
0.1 0 0.1
[1] 1qhs.a 1.0 0.1 -
0
0 0
[1] 1qhx.a 1.9 0.1 - 0.3
0.1
0.2
[1] 1qhy.a 1.2 0 - 0 0
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
1grq.a
1grr.a
1qhn.a
1qhs.a
1qhx.a
1qhy.a
[1] 1grq.a
0
.03 .04 .04 .09 .04
[1] 1grr.a .03
0
.02 .04 .07 .02
[1] 1qhn.a .04 .02
0
.05 .07 .02
[1] 1qhs.a .04 .04 .05
0
.09 .04
[1] 1qhx.a .09 .07 .07 .09
0
.06
[1] 1qhy.a .04 .02 .02 .04 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
1grq.a
1grr.a
1qhn.a
1qhs.a
1qhx.a
1qhy.a
[1] 1grq.a
0
0.8 0.3 0.8 0.7 0.7
[1] 1grr.a 0.8
0
0.8 0.2 0.6 0.3
[1] 1qhn.a 0.3 0.8
0
0.8 0.8 0.8
[1] 1qhs.a 0.8 0.2 0.8
0
0.6 0.2
[1] 1qhx.a 0.7 0.6 0.8 0.6
0
0.4
[1] 1qhy.a 0.7 0.3 0.8 0.2 0.4
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
1grq.a
1grr.a
1qhn.a
1qhs.a
1qhx.a
1qhy.a
[1] 1grq.a
0
2.3 0.9 2.3 2.5 2.3
[1] 1grr.a 2.3
0
2.0 0.6 0.9 0.7
[1] 1qhn.a 0.9 2.0
0
2.1 2.2 2.1
[1] 1qhs.a 2.3 0.6 2.1
0
0.9 0.6
[1] 1qhx.a 2.5 0.9 2.2 0.9
0
0.8
[1] 1qhy.a 2.3 0.7 2.1 0.6 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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