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DRTS_PLAVI_1_238

Bifunctional dihydrofolate reductase-thymidylate synthase

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DRTS_PLAVI):D: DHFR (13:15, 45, 53, 54, 57, 113, 117, 120, 121, 173, 194)
R: Substrate binding (13, 14)
13:15, 45, 53, 54, 57, 113, 117, 120, 121, 173, 194
Cofactors (cF):ndp

Full PDB list

2bl9, 2bla, 2blb, 2blc

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
I
1
3
C
1
4
A
1
5
L
4
5
D
5
3
M
5
4
F
5
7
S
1
1
7
S
1
2
0
I
1
2
1
I
1
7
3
T
1
9
4
[1]2bl9.a cp617 . . . . . . . . . . . . ndp
[1]2bla.a cp617 . . . . . . . N . . . . ndp
[1]2blb.a cp716 . . . . . . . . . . . . ndp
[1]2blc.a cp716 . . . . . . . N . . . . 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

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PDB.ch
A1 cF
I
1
3
C
1
4
A
1
5
L
4
5
D
5
3
M
5
4
F
5
7
M
1
1
3
S
1
1
7
S
1
2
0
I
1
2
1
I
1
7
3
T
1
9
4
[1]2bl9.a . . . . . . . . . . . . . ndp
[1]2bla.a . . . . . . . . N . . . . ndp
[1]2blb.a . . . . . . . . . . . . . ndp
[1]2blc.a . . . . . . . . N . . . . 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
2bl9.a:cp6
2bla.a:cp6
2blb.a:cp7
2blc.a:cp7
[1] 2bl9.a
0.1
0.2 0 0.1
[1] 2bla.a 0.2
0
0 0.1
[1] 2blb.a 0.1 0.2
0
0.1
[1] 2blc.a 0.5 0.7 0.1
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
2bl9.a
2bla.a
2blb.a
2blc.a
[1] 2bl9.a
0
.03 .01 .06
[1] 2bla.a .03
0
.02 .06
[1] 2blb.a .01 .02
0
.05
[1] 2blc.a .06 .06 .05
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
2bl9.a
2bla.a
2blb.a
2blc.a
[1] 2bl9.a
0
0.7 0.3 0.3
[1] 2bla.a 0.7
0
0.8 0.9
[1] 2blb.a 0.3 0.8
0
0.3
[1] 2blc.a 0.3 0.9 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2bl9.a
2bla.a
2blb.a
2blc.a
[1] 2bl9.a
0
1.0 0.5 0.6
[1] 2bla.a 1.0
0
1.0 1.1
[1] 2blb.a 0.5 1.0
0
0.4
[1] 2blc.a 0.6 1.1 0.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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