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DYR_THEMA_2_169

Dihydrofolate reductase [Dihydrofolate reductase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DYR_THEMA):D: DHFR (7:9, 28:30, 32, 33, 51, 52, 54, 56, 59, 101, 122)
R: Substrate binding (7, 8)
R: Substrate binding (28:30)
7:9, 28:30, 32, 33, 51, 52, 54, 56, 59, 101, 122
Cofactors (cF):ndp

Full PDB list

1cz3, 1d1g

Pocket contact map

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PDB.ch
   
ligand
A1 cF
V
7
L
8
A
9
D
2
8
R
2
9
K
3
0
F
3
2
R
3
3
E
5
1
I
5
2
R
5
4
L
5
6
R
5
9
I
1
0
1
[1]1cz3.a none . . . . . . . . . . . . . .
[1]1d1g.a mtx33 . . . . . . . . . . . . . . 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
V
7
L
8
A
9
D
2
8
R
2
9
K
3
0
F
3
2
R
3
3
E
5
1
I
5
2
R
5
4
L
5
6
R
5
9
I
1
0
1
T
1
2
2
[1]1cz3.a . . . . . . . * . . . . . . .
[1]1d1g.a . . . . . . . . . . . . . . . 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
1cz3.a is apo
1d1g.a:mtx
[1] 1cz3.a
-
1.2
[1] 1d1g.a -
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
1cz3.a
1d1g.a
[1] 1cz3.a
0
.08
[1] 1d1g.a .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1cz3.a
1d1g.a
[1] 1cz3.a
0
0.4
[1] 1d1g.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

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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
1cz3.a
1d1g.a
[1] 1cz3.a
0
1.5
[1] 1d1g.a 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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