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DPOL_BPR69_1_903

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

Composition of the binding site

Protein chains monomer
A1 (DPOL_BPR69):2, 33, 34, 36, 59, 61, 95, 98, 99, 3742, 33, 34, 36, 59, 61, 95, 98, 99, 374

Full PDB list

1clq, 1ig9, 1ih7, 1q9x, 1q9y, 1waf, 1waj, 2atq, 2dtu, 2dy4, 2oyq, 2ozm, 2ozs, 2p5g, 2p5o, 3cfo, 3cfp, 3cfr, 3cq8, 3l8b, 3lds, 3lzi, 3lzj, 3nae, 3nci, 3ndk, 3ne6, 3ngi, 3qei, 3qep, 3qer, 3qes, 3qev, 3qew, 3qex, 3qnn, 3qno, 3rma, 3rmb, 3rmc, 3rmd, 3rwu, 3s9h, 3scx, 3si6, 3sjj, 3spy, 3spz, 3sq0, 3sq1, 3sq2, 3sq4, 3sun, 3suo, 3sup, 3suq, 3tab, 3tae, 3taf, 3tag, 4dtj, 4dtn, 4dtp, 4dtr, 4dtu, 4du1, 4du3, 4du4, 4e3s, 4fj5, 4fj7, 4fj9, 4fjh, 4fjl, 4fk0, 4fk4, 4i9l, 4i9q, 4khn, 5gnq (redundant Pocketome entry); 3kd1, 3kd5, 3nhg, 3qet, 3snn, 3uiq, 4dtm, 4dto, 4dts, 4dtx, 4fj8, 4fjg, 4fji, 4fjj, 4fjk, 4fjm, 4fjn, 4fjx, 4fk2, 4j2a, 4j2b, 4j2d, 4j2e, 4khq, 4khs, 4khu, 4khw, 4khy, 4ki4, 4ki6, 4m3r, 4m3t, 4m3u, 4m3w, 4m3x, 4m3y, 4m3z, 4m41, 4m42, 4m45 (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
2
Y
3
3
K
3
4
R
5
9
L
6
1
D
9
5
N
9
8
Y
9
9
K
3
7
4
[1]1q9x.a dgp22 . . . . . . . . .
[1]2oyq.a G,n5p51 . . . . . . . . .
[1]2p5g.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
K
2
Y
3
3
K
3
4
S
3
6
R
5
9
L
6
1
D
9
5
N
9
8
Y
9
9
K
3
7
4
[1]1q9x.a . . . . . . . . . .
[1]2oyq.a . . . . . . . . . .
[1]2p5g.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
1q9x.a:dgp
2oyq.a:G,n5p
2p5g.a is apo
[1] 1q9x.a
0.1
0.9 -
[1] 2oyq.a 0.3
0.1
-
[1] 2p5g.a 0.3 0.2
-
[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
1q9x.a
2oyq.a
2p5g.a
[1] 1q9x.a
0
.09 .10
[1] 2oyq.a .09
0
.01
[1] 2p5g.a .10 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1q9x.a
2oyq.a
2p5g.a
[1] 1q9x.a
0
0.5 0.4
[1] 2oyq.a 0.5
0
0.2
[1] 2p5g.a 0.4 0.2
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
1q9x.a
2oyq.a
2p5g.a
[1] 1q9x.a
0
1.2 1.2
[1] 2oyq.a 1.2
0
0.7
[1] 2p5g.a 1.2 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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