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DYR21_ECOLX_17_78

Dihydrofolate reductase type 2

Composition of the binding site

Protein chains homotetramer
A1 (DYR21_ECOLX):32, 36, 66:6932, 36, 66:69
A2 (DYR21_ECOLX):32, 34:36, 50, 69, 70, 72, 7332, 34:36, 50, 69, 70, 72, 73
A3 (DYR21_ECOLX):6868
A4 (DYR21_ECOLX):64:6764:67

Full PDB list

1vie, 1vif, 2gqv, 2p4t, 2rh2, 2rk1, 2rk2, 3sfm (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 A3 A4
K
3
2
A
3
6
V
6
6
Q
6
7
I
6
8
Y
6
9
K
3
2
G
3
5
A
3
6
L
5
0
P
7
0
A
7
2
A
7
3
I
6
8
G
6
4
S
6
5
V
6
6
Q
6
7
[1]1vif.a fol13 . . . . . . . . . . . . . . . . . .
[1]2p4t.a nap26 . . . H . . . . . . . . . . . . . H
[1]2rk1.a nap48 . . . . . . . . . . . . . . . . . .
[1]3sfm.a none . . . . . . . . . . . . . . . . . .

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 A2 A3 A4
K
3
2
A
3
6
V
6
6
Q
6
7
I
6
8
Y
6
9
K
3
2
S
3
4
G
3
5
A
3
6
L
5
0
Y
6
9
P
7
0
A
7
2
A
7
3
I
6
8
G
6
4
S
6
5
V
6
6
Q
6
7
[1]1vif.a . . . . . . . . . . . . . . . . . . . .
[1]2p4t.a . . . H . . . . . . . . . . . . . . . H
[1]2rk1.a . . . . . . . . . . . . . . . . . . . .
[1]3sfm.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
1vif.a:fol
2p4t.a:nap
2rk1.a:nap
3sfm.a is apo
[1] 1vif.a
0
0.1 0.1 -
[1] 2p4t.a 0
0
0.2 -
[1] 2rk1.a 0 0
0
-
[1] 3sfm.a 0.4 0.4 0.4
-
[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
1vif.a
2p4t.a
2rk1.a
3sfm.a
[1] 1vif.a
0
.02 .01 .02
[1] 2p4t.a .02
0
.01 .04
[1] 2rk1.a .01 .01
0
.03
[1] 3sfm.a .02 .04 .03
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
1vif.a
2p4t.a
2rk1.a
3sfm.a
[1] 1vif.a
0
0.6 0.3 0.3
[1] 2p4t.a 0.6
0
0.5 0.7
[1] 2rk1.a 0.3 0.5
0
0.2
[1] 3sfm.a 0.3 0.7 0.2
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
1vif.a
2p4t.a
2rk1.a
3sfm.a
[1] 1vif.a
0
0.7 0.6 0.6
[1] 2p4t.a 0.7
0
0.6 0.7
[1] 2rk1.a 0.6 0.6
0
0.4
[1] 3sfm.a 0.6 0.7 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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