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DHYS_HUMAN_2_369

Deoxyhypusine synthase [Deoxyhypusine synthase family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (DHYS_HUMAN):R: Spermidine binding (314:316)
R: Spermidine binding (323, 327, 329)
288, 292, 295, 319
288, 292, 295, 314:316, 319, 323, 327, 329
A2 (DHYS_HUMAN):106, 166, 167, 239, 240, 243106, 166, 167, 239, 240, 243

Full PDB list

1dhs, 1rlz, 1roz, 1rqd (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
H
2
8
8
N
2
9
2
L
2
9
5
G
3
1
4
S
3
1
5
D
3
1
6
A
3
1
9
E
3
2
3
W
3
2
7
K
3
2
9
N
1
0
6
I
1
6
6
D
2
4
3
[1]1dhs.a none . . . . . . . . . . . . .
[1]1rqd.a gc712 . . . . . . . . . . . . .

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 A2
H
2
8
8
N
2
9
2
L
2
9
5
G
3
1
4
S
3
1
5
D
3
1
6
A
3
1
9
E
3
2
3
W
3
2
7
K
3
2
9
N
1
0
6
I
1
6
6
G
1
6
7
G
2
3
9
S
2
4
0
D
2
4
3
[1]1dhs.a . . . . . . . . . . . . . . . .
[1]1rqd.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
1dhs.a is apo
1rqd.a:gc7
[1] 1dhs.a
-
0.8
[1] 1rqd.a -
0.2
[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
1dhs.a
1rqd.a
[1] 1dhs.a
0
.05
[1] 1rqd.a .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1dhs.a
1rqd.a
[1] 1dhs.a
0
0.3
[1] 1rqd.a 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
1dhs.a
1rqd.a
[1] 1dhs.a
0
0.6
[1] 1rqd.a 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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