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DRTS_PLAFK_1_608

Bifunctional dihydrofolate reductase-thymidylate synthase

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DRTS_PLAFK):D: DHFR (14:16, 45, 46, 48, 54, 55, 58, 59, 104, 108, 111:113, 116, 119, 122, 164, 170, 185)
R: Substrate binding (14, 15)
14:16, 45, 46, 48, 54, 55, 58, 59, 104, 108, 111:113, 116, 119, 122, 164, 170, 185
Cofactors (cF):nap.ump/ndp/ndp.ump

Full PDB list

1j3i, 1j3j, 1j3k, 3dg8, 3dga, 3jsu, 3qg2, 3qgt, 3um5, 3um6, 3um8, 4dp3, 4dpd, 4dph

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
I
1
4
C
1
5
A
1
6
L
4
6
D
5
4
M
5
5
F
5
8
R
5
9
M
1
0
4
N
1
0
8
S
1
1
1
I
1
1
2
P
1
1
3
F
1
1
6
L
1
1
9
R
1
2
2
I
1
6
4
Y
1
7
0
T
1
8
5
[1]1j3i.a wra24 . . . . . . . C . S . . . . . . . . . ndp
[1]1j3j.a cp617 . . . . . . . . . . . . . . . . . . . ndp
[1]1j3k.a wra24 . . . . . . . . . . . . . . . . L . . ndp
[1]3dg8.b rj617 . . . . . . . . . . . . . . . . L . . ndp
[1]3dga.a rj118 . . . . . . . C . S . . . . . . . . . ndp
[1]3jsu.a ka525 . . . . . . . . . . . . . . . . L . . ndp.ump
[1]3qg2.a cp617 . . . . . . . . . . . . . . . . L . . ndp.ump
[1]3qgt.a cp617 . . . . . . . C . S . . . . . . . . . ndp.ump
[1]3um5.a cp617 . . V . . . . C . T . . . . . . . . . ndp.ump
[1]3um6.a 1cy17 . . V . . . . C . T . . . . . . . . . ndp.ump
[1]3um8.a 1cy17 . . . . . . . C . S . . . . . . . . . ndp
[1]4dp3.a mmv26 . . . . . . . . . . . . . . . . L . . ndp
[1]4dpd.a dhf32 . . . . . . . C . S . . . . . . . . . nap.ump
[1]4dpd.b none . . . . . . . C . S . . . . . . . . .
[1]4dph.a p6523 . . . . . . . . . . . . . . . . L . . ndp

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
I
1
4
C
1
5
A
1
6
V
4
5
L
4
6
W
4
8
D
5
4
M
5
5
F
5
8
R
5
9
M
1
0
4
N
1
0
8
S
1
1
1
I
1
1
2
P
1
1
3
F
1
1
6
L
1
1
9
R
1
2
2
I
1
6
4
Y
1
7
0
T
1
8
5
[1]1j3i.a . . . . . . . . . C . S . . . . . . . . . ndp
[1]1j3j.a . . . . . . . . . . . . . . . . . . . . . ndp
[1]1j3k.a . . . . . . . . . . . . . . . . . . L . . ndp
[1]3dg8.b . . . . . . . . . . . . . . . . . . L . . ndp
[1]3dga.a . . . . . . . . . C . S . . . . . . . . . ndp
[1]3jsu.a . . . . . . . . . . . . . * . . . . L . . ndp.ump
[1]3qg2.a . . . . . . . . . . . . . . . . . . L . . ndp.ump
[1]3qgt.a . . . . . . . . . C . S . . . . . . . . . ndp.ump
[1]3um5.a . . V . . . . . . C . T . . . . . . . . . ndp.ump
[1]3um6.a . . V . . . . . . C . T . . . . . . . . . ndp.ump
[1]3um8.a . . . . . . . . . C . S . . . . . . . . . ndp
[1]4dp3.a . . . . . . . . . . . . . * . . . . L . . ndp
[1]4dpd.a . . . . . . . . . C . S . . . . . . . . . nap.ump
[1]4dpd.b . . . . . . . . . C . S . . . . . . . . .
[1]4dph.a . . . . . . . . . . . . . . . . . . L . . ndp

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
1j3i.a:wra
1j3j.a:cp6
1j3k.a:wra
3dg8.b:rj6
3dga.a:rj1
3jsu.a:ka5
3qg2.a:cp6
3qgt.a:cp6
3um5.a:cp6
3um6.a:1cy
3um8.a:1cy
4dp3.a:mmv
4dpd.a:dhf
4dpd.b is apo
4dph.a:p65
[1] 1j3i.a
0
0.4 0 0.5 0.6 0 0.3 0.3 0.3 0.7 0.3 0 0.4 - 0
[1] 1j3j.a 0
0
0 0.6 0.4 0 0 0 0 0.3 0.1 0.1 0.2 - 0
[1] 1j3k.a 0.1 0.7
0
0.6 0.6 0 0.7 0.7 0.4 0.8 0.7 0.1 0.5 - 0
[1] 3dg8.b 0 0.1 0
0
0.1 0 0.3 0.1 0.1 0.4 0.4 0 0 - 0
[1] 3dga.a 0 0.1 0 0.2
0.3
0.1 0.1 0.1 0.2 0.5 0.1 0 0.6 - 0
[1] 3jsu.a 0 1.0 0.1 0.6 0.6
0
0.8 0.9 0.6 1.5 0.6 0.1 0.3 - 0.1
[1] 3qg2.a 0 0.1 0 0.5 0.3 0
0.1
0 0 0.3 0.1 0 0.1 - 0
[1] 3qgt.a 0 0.1 0 0.5 0.4 0.1 0.1
0
0 0.6 0.1 0 0.3 - 0
[1] 3um5.a 0.1 0.2 0.1 0.7 0.5 0.1 0.2 0.2
0.1
0.4 0.3 0 0.2 - 0
[1] 3um6.a 0.1 0.1 0.1 0.7 0.5 0.1 0.3 0.1 0.1
0
0.4 0.1 0.2 - 0
[1] 3um8.a 0 0.1 0 0.4 0.6 0 0.1 0.1 0.1 0.2
0
0 0.1 - 0
[1] 4dp3.a 0.1 1.0 0 0.7 0.6 0 1.0 0.8 0.7 1.1 0.7
0
1.0 - 0
[1] 4dpd.a 0 0 0 0.4 0.1 0 0 0 0 0.3 0 0
0
- 0
[1] 4dpd.b 0 0.1 0 0.5 0.4 0.1 0.1 0.1 0.1 0.4 0.1 0.1 0.1
-
0
[1] 4dph.a 0.1 0.6 0 0.8 0.4 0.1 0.6 0.6 0.3 0.7 0.6 0.1 0.7 -
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
1j3i.a
1j3j.a
1j3k.a
3dg8.b
3dga.a
3jsu.a
3qg2.a
3qgt.a
3um5.a
3um6.a
3um8.a
4dp3.a
4dpd.a
4dpd.b
4dph.a
[1] 1j3i.a
0
.05 .05 .09 .06 .07 .05 .03 .06 .08 .06 .08 .06 .06 .05
[1] 1j3j.a .05
0
.08 .04 .06 .11 .01 .02 .02 .05 .02 .11 .02 .01 .09
[1] 1j3k.a .05 .08
0
.09 .06 .05 .07 .07 .08 .08 .09 .06 .08 .08 .02
[1] 3dg8.b .09 .04 .09
0
.07 .11 .04 .05 .05 .07 .07 .12 .03 .04 .10
[1] 3dga.a .06 .06 .06 .07
0
.11 .06 .05 .08 .10 .07 .10 .06 .06 .05
[1] 3jsu.a .07 .11 .05 .11 .11
0
.10 .10 .11 .11 .12 .07 .11 .11 .07
[1] 3qg2.a .05 .01 .07 .04 .06 .10
0
.03 .02 .05 .02 .10 .01 .02 .08
[1] 3qgt.a .03 .02 .07 .05 .05 .10 .03
0
.04 .07 .04 .10 .04 .03 .08
[1] 3um5.a .06 .02 .08 .05 .08 .11 .02 .04
0
.04 .02 .11 .03 .03 .09
[1] 3um6.a .08 .05 .08 .07 .10 .11 .05 .07 .04
0
.04 .11 .06 .05 .09
[1] 3um8.a .06 .02 .09 .07 .07 .12 .02 .04 .02 .04
0
.12 .03 .03 .10
[1] 4dp3.a .08 .11 .06 .12 .10 .07 .10 .10 .11 .11 .12
0
.10 .12 .06
[1] 4dpd.a .06 .02 .08 .03 .06 .11 .01 .04 .03 .06 .03 .10
0
.02 .08
[1] 4dpd.b .06 .01 .08 .04 .06 .11 .02 .03 .03 .05 .03 .12 .02
0
.10
[1] 4dph.a .05 .09 .02 .10 .05 .07 .08 .08 .09 .09 .10 .06 .08 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1j3i.a
1j3j.a
1j3k.a
3dg8.b
3dga.a
3jsu.a
3qg2.a
3qgt.a
3um5.a
3um6.a
3um8.a
4dp3.a
4dpd.a
4dpd.b
4dph.a
[1] 1j3i.a
0
0.3 0.3 0.7 0.4 0.4 0.4 0.3 0.5 0.6 0.2 0.5 0.2 0.5 0.4
[1] 1j3j.a 0.3
0
0.5 0.7 0.5 0.5 0.4 0.2 0.5 0.6 0.2 0.6 0.3 0.4 0.6
[1] 1j3k.a 0.3 0.5
0
0.5 0.4 0.2 0.2 0.4 0.4 0.5 0.4 0.2 0.4 0.6 0.2
[1] 3dg8.b 0.7 0.7 0.5
0
0.6 0.5 0.5 0.6 0.5 0.6 0.6 0.6 0.6 0.7 0.6
[1] 3dga.a 0.4 0.5 0.4 0.6
0
0.3 0.4 0.4 0.3 0.4 0.4 0.5 0.4 0.6 0.5
[1] 3jsu.a 0.4 0.5 0.2 0.5 0.3
0
0.3 0.5 0.4 0.6 0.4 0.3 0.4 0.6 0.3
[1] 3qg2.a 0.4 0.4 0.2 0.5 0.4 0.3
0
0.4 0.3 0.5 0.4 0.3 0.4 0.5 0.3
[1] 3qgt.a 0.3 0.2 0.4 0.6 0.4 0.5 0.4
0
0.4 0.5 0.2 0.6 0.2 0.3 0.5
[1] 3um5.a 0.5 0.5 0.4 0.5 0.3 0.4 0.3 0.4
0
0.2 0.4 0.5 0.4 0.5 0.5
[1] 3um6.a 0.6 0.6 0.5 0.6 0.4 0.6 0.5 0.5 0.2
0
0.5 0.7 0.5 0.5 0.7
[1] 3um8.a 0.2 0.2 0.4 0.6 0.4 0.4 0.4 0.2 0.4 0.5
0
0.6 0.2 0.3 0.5
[1] 4dp3.a 0.5 0.6 0.2 0.6 0.5 0.3 0.3 0.6 0.5 0.7 0.6
0
0.6 0.7 0.2
[1] 4dpd.a 0.2 0.3 0.4 0.6 0.4 0.4 0.4 0.2 0.4 0.5 0.2 0.6
0
0.3 0.5
[1] 4dpd.b 0.5 0.4 0.6 0.7 0.6 0.6 0.5 0.3 0.5 0.5 0.3 0.7 0.3
0
0.7
[1] 4dph.a 0.4 0.6 0.2 0.6 0.5 0.3 0.3 0.5 0.5 0.7 0.5 0.2 0.5 0.7
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

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
1j3i.a
1j3j.a
1j3k.a
3dg8.b
3dga.a
3jsu.a
3qg2.a
3qgt.a
3um5.a
3um6.a
3um8.a
4dp3.a
4dpd.a
4dpd.b
4dph.a
[1] 1j3i.a
0
0.5 0.4 0.8 0.4 0.5 0.6 0.4 0.5 0.6 0.5 0.5 0.5 0.6 0.5
[1] 1j3j.a 0.5
0
0.7 0.9 0.6 0.7 0.4 0.2 0.5 0.7 0.5 0.9 0.4 0.7 0.8
[1] 1j3k.a 0.4 0.7
0
0.8 0.5 0.4 0.6 0.6 0.6 0.7 0.5 0.6 0.6 0.7 0.5
[1] 3dg8.b 0.8 0.9 0.8
0
0.7 0.9 0.8 0.7 0.6 0.8 0.6 1.0 0.6 0.8 0.9
[1] 3dga.a 0.4 0.6 0.5 0.7
0
0.5 0.6 0.5 0.5 0.6 0.6 0.5 0.6 0.7 0.6
[1] 3jsu.a 0.5 0.7 0.4 0.9 0.5
0
0.6 0.6 0.6 0.7 0.6 0.7 0.6 0.7 0.6
[1] 3qg2.a 0.6 0.4 0.6 0.8 0.6 0.6
0
0.4 0.4 0.6 0.5 0.8 0.5 0.7 0.7
[1] 3qgt.a 0.4 0.2 0.6 0.7 0.5 0.6 0.4
0
0.4 0.6 0.4 0.7 0.4 0.6 0.7
[1] 3um5.a 0.5 0.5 0.6 0.6 0.5 0.6 0.4 0.4
0
0.3 0.5 0.7 0.5 0.6 0.7
[1] 3um6.a 0.6 0.7 0.7 0.8 0.6 0.7 0.6 0.6 0.3
0
0.6 0.8 0.6 0.6 0.8
[1] 3um8.a 0.5 0.5 0.5 0.6 0.6 0.6 0.5 0.4 0.5 0.6
0
0.7 0.3 0.6 0.7
[1] 4dp3.a 0.5 0.9 0.6 1.0 0.5 0.7 0.8 0.7 0.7 0.8 0.7
0
0.8 0.8 0.7
[1] 4dpd.a 0.5 0.4 0.6 0.6 0.6 0.6 0.5 0.4 0.5 0.6 0.3 0.8
0
0.6 0.7
[1] 4dpd.b 0.6 0.7 0.7 0.8 0.7 0.7 0.7 0.6 0.6 0.6 0.6 0.8 0.6
0
0.8
[1] 4dph.a 0.5 0.8 0.5 0.9 0.6 0.6 0.7 0.7 0.7 0.8 0.7 0.7 0.7 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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