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DPOL_BPT7_1_704

DNA-directed DNA polymerase [DNA polymerase type-A family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DPOL_BPT7):R: Polymerase (429, 475:480, 506, 518, 522, 523, 526, 527, 529:536, 539, 540, 607, 654)429, 475:480, 506, 518, 522, 523, 526, 527, 529:536, 539, 540, 607, 654

Full PDB list

1skr, 1sks, 1skw, 1sl0, 1sl1, 1sl2, 1t7p, 1t8e, 1tk0, 1tk5, 1tk8, 1tkd, 1x9m, 1x9s, 1x9w, 1zyq, 2ajq (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
4
2
9
D
4
7
5
A
4
7
6
S
4
7
7
G
4
7
8
L
4
7
9
E
4
8
0
H
5
0
6
R
5
1
8
K
5
2
2
Y
5
2
6
G
5
2
7
Y
5
3
0
G
5
3
1
A
5
3
2
G
5
3
3
K
5
3
6
H
6
0
7
D
6
5
4
[1]1skr.a dad,mg30 . . . . . . . . . . . . . . . . . . .
[1]1sl2.a dad,mg,mg31 . . . . . . . . . . . . . - - - . . .
[1]1t7p.a dg3,mg,mg32 . . . . . . . . . . . . . . . . . . .
[1]1t8e.a dct,G,mg50 . . . . . . . . . . . . . . . . . . .
[1]1tk0.a 8og,dct,mg,mg52 . . . . . . . . . . . . . . . . . . .
[1]1tk8.a A,d3t,mg,mg51 . . . . . . . . . . . . . . . . . . .
[1]1tkd.a d3t,mg,mg30 . . . . . . . . . . . . . . . . . . .
[1]1zyq.a dad,mg30 . . . . . . . . . . . . . . . . A . .
[1]2ajq.a G22 . . . . . . . . . . . . . . . . . . .
[2]1sl1.a ttd35 . . . . . . . . . . . . . . . . . . .
[3]1sks.a 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
4
2
9
D
4
7
5
A
4
7
6
S
4
7
7
G
4
7
8
L
4
7
9
E
4
8
0
H
5
0
6
R
5
1
8
K
5
2
2
T
5
2
3
Y
5
2
6
G
5
2
7
L
5
2
9
Y
5
3
0
G
5
3
1
A
5
3
2
G
5
3
3
D
5
3
4
E
5
3
5
K
5
3
6
Q
5
3
9
I
5
4
0
H
6
0
7
D
6
5
4
[1]1skr.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1sl2.a . . . . . . . . . . . . . . . - - - . . . . . . .
[1]1t7p.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1t8e.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1tk0.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1tk8.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1tkd.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zyq.a . . . . . . . . . . . . . . . . . . . . A . . . .
[1]2ajq.a . . . . . . . . . . . . . . . . . . . . . . . . *
[2]1sl1.a . . . . . . * . . . . . . . * . * * . . . . . . .
[3]1sks.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
1skr.a:dad,mg
1sl2.a:dad,mg
1t7p.a:dg3,mg
1t8e.a:G,dct,mg
1tk0.a:8og,dct,mg
1tk8.a:A,d3t,mg
1tkd.a:d3t,mg
1zyq.a:dad,mg
2ajq.a:G
1sl1.a:ttd
1sks.a is apo
[1] 1skr.a
0.3
0.3 0.4 0.2 0.5 0.3 0.3 0.4 0 0.2 -
[1] 1sl2.a 0.6
0.5
0.5 0.3 0.6 0.5 0.6 0.7 0 0.2 -
[1] 1t7p.a 0.3 0.4
0.4
0.3 0.6 0.3 0.2 0.4 0 0.3 -
[1] 1t8e.a 0.7 0.5 0.6
0.5
0.7 0.6 0.7 0.8 0 0.5 -
[1] 1tk0.a 0.5 0.7 0.6 0.7
0.5
0.7 0.8 0.5 0 0.7 -
[1] 1tk8.a 0.6 0.4 0.6 0.4 0.8
0.5
0.6 0.6 0 0.5 -
[1] 1tkd.a 0.3 0.4 0.6 0.5 0.6 0.6
0.3
0.7 0 0.2 -
[1] 1zyq.a 0.4 0.4 0.4 0.6 0.6 0.4 0.3
0.2
0.1 0.2 -
[1] 2ajq.a 0.9 1.6 1.5 1.2 1.7 1.2 0.6 1.2
0.1
0 -
[2] 1sl1.a 1.3 1.5 1.7 7.3 7.7 7.0 0.7 2.2 4.9
0
-
[3] 1sks.a 2.0 2.4 3.5 13 14 13 1.2 2.4 9.3 2.4
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 clusters)

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
1skr.a
1sl2.a
1t7p.a
1t8e.a
1tk0.a
1tk8.a
1tkd.a
1zyq.a
2ajq.a
1sl1.a
1sks.a
[1] 1skr.a
0
.02 .02 .04 .06 .03 .02 .03 .08 .35 .56
[1] 1sl2.a .02
0
.02 .05 .05 .03 .03 .05 .09 .36 .57
[1] 1t7p.a .02 .02
0
.03 .04 .03 .02 .03 .09 .35 .57
[1] 1t8e.a .04 .05 .03
0
.05 .04 .04 .05 .10 .37 .58
[1] 1tk0.a .06 .05 .04 .05
0
.04 .04 .05 .12 .38 .60
[1] 1tk8.a .03 .03 .03 .04 .04
0
.03 .05 .10 .35 .57
[1] 1tkd.a .02 .03 .02 .04 .04 .03
0
.03 .10 .35 .58
[1] 1zyq.a .03 .05 .03 .05 .05 .05 .03
0
.09 .34 .56
[1] 2ajq.a .08 .09 .09 .10 .12 .10 .10 .09
0
.35 .49
[2] 1sl1.a .35 .36 .35 .37 .38 .35 .35 .34 .35
0
.33
[3] 1sks.a .56 .57 .57 .58 .60 .57 .58 .56 .49 .33
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1skr.a
1sl2.a
1t7p.a
1t8e.a
1tk0.a
1tk8.a
1tkd.a
1zyq.a
2ajq.a
1sl1.a
1sks.a
[1] 1skr.a
0
0.4 0.2 0.3 0.2 0.3 0.2 0.4 3.3 3.7 3.7
[1] 1sl2.a 0.4
0
0.3 0.3 0.3 0.3 0.4 0.4 3.6 3.5 3.5
[1] 1t7p.a 0.2 0.3
0
0.2 0.2 0.3 0.2 0.5 3.4 3.7 3.8
[1] 1t8e.a 0.3 0.3 0.2
0
0.3 0.3 0.3 0.5 3.4 3.7 3.7
[1] 1tk0.a 0.2 0.3 0.2 0.3
0
0.2 0.2 0.4 3.3 3.6 3.7
[1] 1tk8.a 0.3 0.3 0.3 0.3 0.2
0
0.3 0.4 3.3 3.5 3.6
[1] 1tkd.a 0.2 0.4 0.2 0.3 0.2 0.3
0
0.4 3.3 3.6 3.7
[1] 1zyq.a 0.4 0.4 0.5 0.5 0.4 0.4 0.4
0
3.2 3.5 3.5
[1] 2ajq.a 3.3 3.6 3.4 3.4 3.3 3.3 3.3 3.2
0
2.5 2.7
[2] 1sl1.a 3.7 3.5 3.7 3.7 3.6 3.5 3.6 3.5 2.5
0
0.6
[3] 1sks.a 3.7 3.5 3.8 3.7 3.7 3.6 3.7 3.5 2.7 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1skr.a
1sl2.a
1t7p.a
1t8e.a
1tk0.a
1tk8.a
1tkd.a
1zyq.a
2ajq.a
1sl1.a
1sks.a
[1] 1skr.a
0
0.7 0.3 0.5 0.4 0.6 0.7 0.5 3.7 4.1 4.3
[1] 1sl2.a 0.7
0
0.7 0.7 0.7 0.4 0.4 0.8 3.8 4.0 4.2
[1] 1t7p.a 0.3 0.7
0
0.4 0.4 0.6 0.7 0.6 3.8 4.1 4.3
[1] 1t8e.a 0.5 0.7 0.4
0
0.5 0.6 0.8 0.6 3.8 4.1 4.3
[1] 1tk0.a 0.4 0.7 0.4 0.5
0
0.5 0.7 0.5 3.8 4.1 4.3
[1] 1tk8.a 0.6 0.4 0.6 0.6 0.5
0
0.4 0.7 3.7 4.0 4.2
[1] 1tkd.a 0.7 0.4 0.7 0.8 0.7 0.4
0
0.8 3.7 4.0 4.2
[1] 1zyq.a 0.5 0.8 0.6 0.6 0.5 0.7 0.8
0
3.6 4.0 4.2
[1] 2ajq.a 3.7 3.8 3.8 3.8 3.8 3.7 3.7 3.6
0
2.6 2.9
[2] 1sl1.a 4.1 4.0 4.1 4.1 4.1 4.0 4.0 4.0 2.6
0
1.1
[3] 1sks.a 4.3 4.2 4.3 4.3 4.3 4.2 4.2 4.2 2.9 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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