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DCPS_HUMAN_37_337

m7GpppX diphosphatase [HIT family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DCPS_HUMAN):R: Substrate binding (268, 271:273, 277, 279)
54, 59, 61, 63, 83, 85, 128, 130, 132, 139:146, 171, 175, 179, 185, 188, 203:207, 217, 219, 288, 289, 294, 322
54, 59, 61, 63, 83, 85, 128, 130, 132, 139:146, 171, 175, 179, 185, 188, 203:207, 217, 219, 268, 271:273, 277, 279, 288, 289, 294, 322

Full PDB list

1st0, 1st4, 1xml, 1xmm, 3bl7, 3bl9, 3bla, 4qde, 4qdv, 4qeb

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
5
4
D
5
9
I
6
1
F
6
3
I
8
3
E
8
5
K
1
2
8
T
1
3
0
V
1
3
2
H
1
3
9
K
1
4
2
Y
1
4
3
L
1
7
1
W
1
7
5
I
1
7
9
E
1
8
5
R
1
8
8
I
2
0
3
P
2
0
4
D
2
0
5
L
2
0
6
K
2
0
7
I
2
1
9
H
2
6
8
P
2
7
1
S
2
7
2
Y
2
7
3
H
2
7
7
H
2
7
9
P
2
8
8
G
2
8
9
R
2
9
4
[1]1st0.a gtg52 . . . . . . . . . . . . . . . . . . . . . . . . . . . N . . . .
[1]1st4.a gta51 . . . . . . . . . . . . . . . . . . . . . . . . . . . N . . . .
[1]1xml.b none . . . . . . . . . . . . . . . . . . . . M . . . . . . . . - - .
[1]1xmm.a m7g29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1xmm.b po4-g7m30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1xmm.c po4.g7m30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3bl7.a dd128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3bl9.a dd229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3bla.a dd322 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4qde.a 30s23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4qdv.a 30u23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4qeb.a 31g23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4qeb.d 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
R
5
4
D
5
9
I
6
1
F
6
3
I
8
3
E
8
5
K
1
2
8
T
1
3
0
V
1
3
2
H
1
3
9
L
1
4
0
Q
1
4
1
K
1
4
2
Y
1
4
3
L
1
4
4
R
1
4
5
Q
1
4
6
L
1
7
1
W
1
7
5
I
1
7
9
E
1
8
5
R
1
8
8
I
2
0
3
P
2
0
4
D
2
0
5
L
2
0
6
K
2
0
7
Y
2
1
7
I
2
1
9
H
2
6
8
P
2
7
1
S
2
7
2
Y
2
7
3
H
2
7
7
H
2
7
9
P
2
8
8
G
2
8
9
R
2
9
4
R
3
2
2
[1]1st0.a . . . . . . . . . . . . * . . . . . . . . . . . . . . . . * . . * N . . . . .
[1]1st4.a . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . * N . . . . .
[1]1xml.b . . . . . . . . . . . . . . . . . . . . . . . . . M . . . . . * . . . - - . .
[1]1xmm.a . . . . . . . . . . . . * . . . . . . . . . . . . . * . . * . . * . . . . . .
[1]1xmm.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1xmm.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]3bl7.a . . . . . . . . . . . . * . . . . . . . . . . . . . * . . . . * * . . . . . .
[1]3bl9.a . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . * * . . . . . .
[1]3bla.a . . . . . . . . . . . . * . . . . . . . . . . . . . * . . . . * * . . . . . .
[1]4qde.a . . . . . . . . . . . . * . . . . . . . . . . . . . * . . . . . * . . . . . .
[1]4qdv.a . . . . . . . . . . . . * . . . . . . . . . . . . . * . . . . * * . . . . . .
[1]4qeb.a . . . . . . . . . . . . * . . . . . . . . . . . . . * . . . . * . . . . . . .
[1]4qeb.d . . . . . . . . . . . . * . . . . . . . . . . . . * . . . . . * . . . . . . .

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
1st0.a:gtg
1st4.a:gta
1xml.b is apo
1xmm.a:m7g
1xmm.b:po4-g7m
1xmm.c:po4.g7m
3bl7.a:dd1
3bl9.a:dd2
3bla.a:dd3
4qde.a:30s
4qdv.a:30u
4qeb.a:31g
4qeb.d is apo
[1] 1st0.a
0.2
0.9 - 0.2 2.5 3.4 1.1 1.6 1.1 2.2 0.4 2.4 -
[1] 1st4.a 1.4
0.3
- 0.2 2.1 2.3 0.8 0.6 1.2 2.2 0.7 2.8 -
[1] 1xml.b 1.2 1.3
-
0.5 0.1 0.2 0.1 0.2 0.4 0.2 0.2 0.1 -
[1] 1xmm.a 1.3 1.2 -
0.2
2.7 3.1 1.9 2.2 1.3 2.3 1.0 2.6 -
[1] 1xmm.b 1.0 0.7 - 0.4
0.3
0.4 0.2 0.2 0.3 0.2 0.2 0.5 -
[1] 1xmm.c 1.1 0.8 - 0.3 0.5
0.2
0.3 0.5 0.5 0.2 0.1 0.2 -
[1] 3bl7.a 4.4 3.6 - 2.3 2.2 1.6
0
0.1 0.3 1.1 0.5 0.8 -
[1] 3bl9.a 4.0 2.9 - 1.9 2.1 1.5 0
0
0.4 0.3 0.1 0.4 -
[1] 3bla.a 4.4 3.5 - 2.5 2.5 1.8 0.5 0.6
0.1
0.2 0.2 0.4 -
[1] 4qde.a 2.2 2.1 - 1.6 3.7 2.8 1.2 1.1 0.5
0
0 2.6 -
[1] 4qdv.a 3.2 3.1 - 2.3 1.5 2.0 0.9 1.4 0.3 0.1
0.4
0.2 -
[1] 4qeb.a 2.7 3.3 - 2.0 2.5 2.8 1.3 1.5 0.4 0.3 0.6
0
-
[1] 4qeb.d 5.4 6.8 - 4.4 4.4 4.6 4.5 4.6 2.9 2.8 3.3 3.4
-
[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
1st0.a
1st4.a
1xml.b
1xmm.a
1xmm.b
1xmm.c
3bl7.a
3bl9.a
3bla.a
4qde.a
4qdv.a
4qeb.a
4qeb.d
[1] 1st0.a
0
.09 .18 .07 .15 .16 .14 .13 .15 .13 .14 .17 .25
[1] 1st4.a .09
0
.18 .09 .14 .16 .14 .12 .15 .10 .15 .17 .29
[1] 1xml.b .18 .18
0
.20 .04 .04 .14 .13 .15 .17 .15 .13 .24
[1] 1xmm.a .07 .09 .20
0
.17 .18 .12 .13 .15 .10 .11 .14 .24
[1] 1xmm.b .15 .14 .04 .17
0
.04 .15 .14 .16 .15 .15 .13 .23
[1] 1xmm.c .16 .16 .04 .18 .04
0
.14 .13 .15 .15 .14 .12 .24
[1] 3bl7.a .14 .14 .14 .12 .15 .14
0
.05 .05 .08 .08 .09 .20
[1] 3bl9.a .13 .12 .13 .13 .14 .13 .05
0
.04 .09 .09 .09 .19
[1] 3bla.a .15 .15 .15 .15 .16 .15 .05 .04
0
.08 .08 .10 .19
[1] 4qde.a .13 .10 .17 .10 .15 .15 .08 .09 .08
0
.08 .10 .24
[1] 4qdv.a .14 .15 .15 .11 .15 .14 .08 .09 .08 .08
0
.04 .19
[1] 4qeb.a .17 .17 .13 .14 .13 .12 .09 .09 .10 .10 .04
0
.17
[1] 4qeb.d .25 .29 .24 .24 .23 .24 .20 .19 .19 .24 .19 .17
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
1st0.a
1st4.a
1xml.b
1xmm.a
1xmm.b
1xmm.c
3bl7.a
3bl9.a
3bla.a
4qde.a
4qdv.a
4qeb.a
4qeb.d
[1] 1st0.a
0
0.4 7.1 0.5 8.5 7.7 1.2 1.1 1.1 1.0 0.9 1.0 1.0
[1] 1st4.a 0.4
0
7.0 0.5 8.5 7.7 1.0 1.0 1.0 0.8 0.8 0.9 0.9
[1] 1xml.b 7.1 7.0
0
7.1 3.2 2.9 7.0 7.0 7.0 7.2 7.0 7.1 7.1
[1] 1xmm.a 0.5 0.5 7.1
0
8.5 7.7 0.9 0.9 0.9 0.7 0.7 0.8 0.7
[1] 1xmm.b 8.5 8.5 3.2 8.5
0
1.2 8.4 8.4 8.5 8.7 8.5 8.5 8.5
[1] 1xmm.c 7.7 7.7 2.9 7.7 1.2
0
7.6 7.6 7.7 7.8 7.7 7.7 7.7
[1] 3bl7.a 1.2 1.0 7.0 0.9 8.4 7.6
0
0.2 0.5 0.7 0.7 0.8 0.9
[1] 3bl9.a 1.1 1.0 7.0 0.9 8.4 7.6 0.2
0
0.4 0.7 0.7 0.8 0.9
[1] 3bla.a 1.1 1.0 7.0 0.9 8.5 7.7 0.5 0.4
0
0.7 0.7 0.8 0.9
[1] 4qde.a 1.0 0.8 7.2 0.7 8.7 7.8 0.7 0.7 0.7
0
0.4 0.5 0.7
[1] 4qdv.a 0.9 0.8 7.0 0.7 8.5 7.7 0.7 0.7 0.7 0.4
0
0.5 0.6
[1] 4qeb.a 1.0 0.9 7.1 0.8 8.5 7.7 0.8 0.8 0.8 0.5 0.5
0
0.7
[1] 4qeb.d 1.0 0.9 7.1 0.7 8.5 7.7 0.9 0.9 0.9 0.7 0.6 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1st0.a
1st4.a
1xml.b
1xmm.a
1xmm.b
1xmm.c
3bl7.a
3bl9.a
3bla.a
4qde.a
4qdv.a
4qeb.a
4qeb.d
[1] 1st0.a
0
0.8 7.2 1.6 8.5 7.7 2.1 2.1 1.9 1.9 2.2 2.2 2.1
[1] 1st4.a 0.8
0
7.1 1.6 8.5 7.7 2.1 2.1 1.9 1.9 2.1 2.1 2.0
[1] 1xml.b 7.2 7.1
0
7.1 3.6 3.3 6.9 6.9 6.9 7.1 7.0 7.0 7.0
[1] 1xmm.a 1.6 1.6 7.1
0
8.3 7.5 1.7 1.7 1.6 1.1 1.2 1.4 1.6
[1] 1xmm.b 8.5 8.5 3.6 8.3
0
1.5 8.3 8.3 8.4 8.5 8.4 8.4 8.3
[1] 1xmm.c 7.7 7.7 3.3 7.5 1.5
0
7.4 7.5 7.5 7.7 7.5 7.5 7.5
[1] 3bl7.a 2.1 2.1 6.9 1.7 8.3 7.4
0
0.5 0.7 1.7 1.7 1.7 1.9
[1] 3bl9.a 2.1 2.1 6.9 1.7 8.3 7.5 0.5
0
0.6 1.6 1.6 1.7 1.8
[1] 3bla.a 1.9 1.9 6.9 1.6 8.4 7.5 0.7 0.6
0
1.5 1.5 1.6 1.7
[1] 4qde.a 1.9 1.9 7.1 1.1 8.5 7.7 1.7 1.6 1.5
0
1.0 1.1 1.5
[1] 4qdv.a 2.2 2.1 7.0 1.2 8.4 7.5 1.7 1.6 1.5 1.0
0
0.8 1.4
[1] 4qeb.a 2.2 2.1 7.0 1.4 8.4 7.5 1.7 1.7 1.6 1.1 0.8
0
1.5
[1] 4qeb.d 2.1 2.0 7.0 1.6 8.3 7.5 1.9 1.8 1.7 1.5 1.4 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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