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DYRA_STAAU_1_161

Dihydrofolate reductase type 1 from Tn4003 [Dihydrofolate reductase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DYRA_STAAU):D: DHFR (6:8, 17:23, 28, 29, 32, 50, 51, 55, 93, 99)
R: Substrate binding (6:8)
6:8, 17:23, 28, 29, 32, 50, 51, 55, 93, 99
Cofactors (cF):ndp

Full PDB list

2w9s, 2w9t

Pocket contact map

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PDB.ch
   
ligand
A1 cF
I
6
V
7
A
8
L
2
1
D
2
8
L
2
9
I
3
2
S
5
0
I
5
1
F
9
3
Y
9
9
[1]2w9s.a top21 . . . . . . . . . . . ndp
[2]2w9t.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

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PDB.ch
A1 cF
I
6
V
7
A
8
Y
1
7
Q
1
8
N
1
9
Q
2
0
L
2
1
P
2
2
W
2
3
D
2
8
L
2
9
I
3
2
S
5
0
I
5
1
L
5
5
F
9
3
Y
9
9
[1]2w9s.a . . . . . . . . . . . . . . . . . . ndp
[2]2w9t.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
2w9s.a:top
2w9t.a is apo
[1] 2w9s.a
0.1
-
[2] 2w9t.a 9.8
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
2w9s.a
2w9t.a
[1] 2w9s.a
0
.54
[2] 2w9t.a .54
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.9 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
2w9s.a
2w9t.a
[1] 2w9s.a
0
4.2
[2] 2w9t.a 4.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.1 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
2w9s.a
2w9t.a
[1] 2w9s.a
0
5.8
[2] 2w9t.a 5.8
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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