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DPOLA_HUMAN_337_1259

DNA polymerase alpha catalytic subunit [DNA polymerase type-B family]

Composition of the binding site

Protein chains monomer
A1 (DPOLA_HUMAN):783:785, 860:865, 922, 950, 951, 954, 955, 957:959, 962, 1003, 1004783:785, 860:865, 922, 950, 951, 954, 955, 957:959, 962, 1003, 1004

Full PDB list

4q5v, 4qcl, 5iud, 6as7

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
7
8
3
R
7
8
4
S
7
8
5
D
8
6
0
F
8
6
1
N
8
6
2
S
8
6
3
L
8
6
4
Y
8
6
5
R
9
2
2
K
9
5
0
L
9
5
1
N
9
5
4
S
9
5
5
Y
9
5
7
G
9
5
8
C
9
5
9
F
9
6
2
T
1
0
0
3
D
1
0
0
4
[1]4q5v.a 2ze24 . . . . . . . . . . . . . . . . . . . .
[1]4qcl.a dcp,G,mg51 . . . . . . . . . . . . . . . . . . . .
[1]5iud.a none . . . . . . . . . . . . . . . . . . . .
[1]6as7.a dcp,G,mg,mg52 . . . . . . . . . . . . . . . . . . . .

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
G
7
8
3
R
7
8
4
S
7
8
5
D
8
6
0
F
8
6
1
N
8
6
2
S
8
6
3
L
8
6
4
Y
8
6
5
R
9
2
2
K
9
5
0
L
9
5
1
N
9
5
4
S
9
5
5
Y
9
5
7
G
9
5
8
C
9
5
9
F
9
6
2
T
1
0
0
3
D
1
0
0
4
[1]4q5v.a . . . . . . . . . . . . . . . . . . . .
[1]4qcl.a . . . . . . . . . . . . . . . . . . . .
[1]5iud.a . . . . . . . . . . . . . . . . . . . .
[1]6as7.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
4q5v.a:2ze
4qcl.a:G,dcp,mg
5iud.a is apo
6as7.a:G,dcp,mg
[1] 4q5v.a
0
0.9 - 1.3
[1] 4qcl.a 1.9
0.3
- 1.0
[1] 5iud.a 0 1.6
-
1.8
[1] 6as7.a 0 0.6 -
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
4q5v.a
4qcl.a
5iud.a
6as7.a
[1] 4q5v.a
0
.14 .06 .07
[1] 4qcl.a .14
0
.18 .11
[1] 5iud.a .06 .18
0
.09
[1] 6as7.a .07 .11 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
4q5v.a
4qcl.a
5iud.a
6as7.a
[1] 4q5v.a
0
1.5 0.8 0.6
[1] 4qcl.a 1.5
0
1.9 1.6
[1] 5iud.a 0.8 1.9
0
0.8
[1] 6as7.a 0.6 1.6 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
4q5v.a
4qcl.a
5iud.a
6as7.a
[1] 4q5v.a
0
1.8 1.4 0.9
[1] 4qcl.a 1.8
0
2.3 1.9
[1] 5iud.a 1.4 2.3
0
1.5
[1] 6as7.a 0.9 1.9 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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