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DPOG1_HUMAN_70_1239

DNA polymerase subunit gamma-1 [DNA polymerase type-A family]

Composition of the binding site

Protein chains monomer
A1 (DPOG1_HUMAN):853, 890:896, 927, 932, 943, 947, 948, 951, 955, 1071:1074, 1135853, 890:896, 927, 932, 943, 947, 948, 951, 955, 1071:1074, 1135
Metals (Me):Mg

Full PDB list

3ikm, 4ztu, 4ztz, 5c51

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
R
8
5
3
D
8
9
0
V
8
9
1
D
8
9
2
S
8
9
3
Q
8
9
4
E
8
9
5
H
9
3
2
R
9
4
3
K
9
4
7
I
9
4
8
Y
9
5
1
D
1
1
3
5
[1]3ikm.a none . . . . . . . . . . . . .
[1]4ztu.a dct27 . . . . . . . . . . . . . Mg
[1]4ztz.a dcp28 . . . . . . . . . . . . . Mg
[1]5c51.a 1ry28 . . . . . . . . . . R . . Mg

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 Me
R
8
5
3
D
8
9
0
V
8
9
1
D
8
9
2
S
8
9
3
Q
8
9
4
E
8
9
5
L
8
9
6
R
9
2
7
H
9
3
2
R
9
4
3
K
9
4
7
I
9
4
8
Y
9
5
1
Y
9
5
5
R
1
0
7
1
T
1
0
7
2
P
1
0
7
3
V
1
0
7
4
D
1
1
3
5
[1]3ikm.a . . . . . . . . . . . . . . . . . . . *
[1]4ztu.a . . . . . . . . . . . . . . . . . . . . Mg
[1]4ztz.a . . . . . . . . . . . . . . . . . . . . Mg
[1]5c51.a . . . . . . . . . . . . R . . . . . . . Mg

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
3ikm.a is apo
4ztu.a:dct
4ztz.a:dcp
5c51.a:1ry
[1] 3ikm.a
-
3.6 3.8 3.8
[1] 4ztu.a -
0
0 0.3
[1] 4ztz.a - 0
0
0.3
[1] 5c51.a - 0.9 1.0
0.8
[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
3ikm.a
4ztu.a
4ztz.a
5c51.a
[1] 3ikm.a
0
.22 .22 .26
[1] 4ztu.a .22
0
0 .06
[1] 4ztz.a .22 0
0
.06
[1] 5c51.a .26 .06 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3ikm.a
4ztu.a
4ztz.a
5c51.a
[1] 3ikm.a
0
11 11 11
[1] 4ztu.a 11
0
0 0.2
[1] 4ztz.a 11 0
0
0.2
[1] 5c51.a 11 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3ikm.a
4ztu.a
4ztz.a
5c51.a
[1] 3ikm.a
0
11 11 11
[1] 4ztu.a 11
0
0 0.4
[1] 4ztz.a 11 0
0
0.4
[1] 5c51.a 11 0.4 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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