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DUT_HUMAN_98_252

Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial [DUTPase family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (DUT_HUMAN):R: Substrate binding (187:190)
153, 155, 170, 186, 193, 196:198, 200
153, 155, 170, 186:190, 193, 196:198, 200
A2 (DUT_HUMAN):R: Substrate binding (173:175)
178, 179, 216, 219
173:175, 178, 179, 216, 219

Full PDB list

1q5h, 1q5u, 2hqu, 3ara, 3arn, 3ehw, 5h4j (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
V
1
5
3
K
1
5
5
A
1
8
6
G
1
8
7
V
1
8
8
I
1
8
9
D
1
9
0
Y
1
9
3
N
1
9
6
V
1
9
7
G
1
9
8
V
2
0
0
R
1
7
3
S
1
7
4
G
1
7
5
A
1
7
8
K
1
7
9
R
2
1
6
Q
2
1
9
[1]1q5h.c dud24 . . . . . . . . . . . . . . . . . . .
[1]1q5u.x none . . . . . . . . . . . . . . . . . . .
[1]3ara.a mkh33 . . . . . . . . . . . . . . . . . . .
[1]3arn.a msj26 . . . . . . . . . . . . . . . . . . .
[1]3ehw.a dup,mg29 . . . . . . . . . . . . . . . . . . .
[1]5h4j.a fkm31 . . . . . . . . . . . . . . . . . . .

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
V
1
5
3
K
1
5
5
V
1
7
0
A
1
8
6
G
1
8
7
V
1
8
8
I
1
8
9
D
1
9
0
Y
1
9
3
N
1
9
6
V
1
9
7
G
1
9
8
V
2
0
0
R
1
7
3
S
1
7
4
G
1
7
5
A
1
7
8
K
1
7
9
R
2
1
6
Q
2
1
9
[1]1q5h.c . . . . . . . . . . . . . . . . . . . .
[1]1q5u.x . . . . . . . . . . . . . . . . . . . .
[1]3ara.a . . . . . . . . . . . . . . . . . . . .
[1]3arn.a . . . . . . . . . . . . . . . . . . . .
[1]3ehw.a . . . . . . . . . . . . . . . . . . . .
[1]5h4j.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
1q5h.c:dud
1q5u.x is apo
3ara.a:mkh
3arn.a:msj
3ehw.a:dup,mg
5h4j.a:fkm
[1] 1q5h.c
0
- 0.2 0.1 0.2 0.1
[1] 1q5u.x 0.1
-
0.1 0 0.2 0
[1] 3ara.a 0 -
0
0 0.4 0.4
[1] 3arn.a 0.1 - 0.2
0
0.4 0.6
[1] 3ehw.a 0.5 - 0.3 0.3
0
0.3
[1] 5h4j.a 0 - 0.3 0 0.2
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
1q5h.c
1q5u.x
3ara.a
3arn.a
3ehw.a
5h4j.a
[1] 1q5h.c
0
.01 .04 .05 .03 .02
[1] 1q5u.x .01
0
.04 .05 .03 .01
[1] 3ara.a .04 .04
0
.02 .07 .05
[1] 3arn.a .05 .05 .02
0
.08 .05
[1] 3ehw.a .03 .03 .07 .08
0
.04
[1] 5h4j.a .02 .01 .05 .05 .04
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
1q5h.c
1q5u.x
3ara.a
3arn.a
3ehw.a
5h4j.a
[1] 1q5h.c
0
0.3 0.4 0.3 0.5 0.3
[1] 1q5u.x 0.3
0
0.3 0.2 0.5 0.2
[1] 3ara.a 0.4 0.3
0
0.1 0.4 0.2
[1] 3arn.a 0.3 0.2 0.1
0
0.5 0.2
[1] 3ehw.a 0.5 0.5 0.4 0.5
0
0.5
[1] 5h4j.a 0.3 0.2 0.2 0.2 0.5
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
1q5h.c
1q5u.x
3ara.a
3arn.a
3ehw.a
5h4j.a
[1] 1q5h.c
0
0.8 1.1 1.0 0.8 0.9
[1] 1q5u.x 0.8
0
0.7 0.8 0.8 0.7
[1] 3ara.a 1.1 0.7
0
0.4 0.9 0.9
[1] 3arn.a 1.0 0.8 0.4
0
1.0 0.8
[1] 3ehw.a 0.8 0.8 0.9 1.0
0
1.0
[1] 5h4j.a 0.9 0.7 0.9 0.8 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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