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DEOD_BACSU_2_233

Purine nucleoside phosphorylase DeoD-type [PNP/UDP phosphorylase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DEOD_BACSU):R: Phosphate binding (87, 90)
R: Purine nucleoside binding (178:180)
R: Purine nucleoside binding (202, 203)
64, 91, 92, 156, 159, 177, 205, 216
64, 87, 90:92, 156, 159, 177:180, 202, 203, 205, 216

Full PDB list

4d8v, 4d8x, 4d8y, 4d98, 4d9h, 4da0, 4da6, 4da7, 4da8, 4dab, 4dae, 4dan, 4dao, 4dar (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
M
6
4
R
8
7
S
9
0
C
9
1
G
9
2
A
1
5
6
F
1
5
9
V
1
7
7
E
1
7
8
M
1
7
9
E
1
8
0
S
2
0
2
D
2
0
3
V
2
0
5
[1]4d98.b none . . . . . . . . . . . . . .
[1]4d9h.a adn19 . . . . . . . . . . . . . .
[1]4da0.a gng19 . . . . . . . . . . . . . .
[1]4da6.a ga218 . . . . . . . . . . . . . .
[1]4da7.a ac216 . . . . . . . . . . . . . .
[1]4da8.a bg221 . . . . . . . . . . . . . .
[1]4dab.a hpa10 . . . . . . . . . . . . . .
[1]4dae.a 6cr20 . . . . . . . . . . . . . .
[1]4dan.a 2fa20 . . . . . . . . . . . . . .
[1]4dao.a ade10 . . . . . . . . . . . . . .
[1]4dar.a tbn19 . . . . . . . . . . . . . .

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
M
6
4
R
8
7
S
9
0
C
9
1
G
9
2
A
1
5
6
F
1
5
9
V
1
7
7
E
1
7
8
M
1
7
9
E
1
8
0
S
2
0
2
D
2
0
3
V
2
0
5
R
2
1
6
[1]4d98.b . . . . . . . . . . . . . . .
[1]4d9h.a . . . . . . . . . . . . . . .
[1]4da0.a . . . . . . . . . . . . . . .
[1]4da6.a . . . . . . . . . . . . . . .
[1]4da7.a . . . . . . . . . . . . . . .
[1]4da8.a . . . . . . . . . . . . . . .
[1]4dab.a . . . . . . . . . . . . . . .
[1]4dae.a . . . . . . . . . . . . . . .
[1]4dan.a . . . . . . . . . . . . . . .
[1]4dao.a . . * . . . . . . . . . . . .
[1]4dar.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
4d98.b is apo
4d9h.a:adn
4da0.a:gng
4da6.a:ga2
4da7.a:ac2
4da8.a:bg2
4dab.a:hpa
4dae.a:6cr
4dan.a:2fa
4dao.a:ade
4dar.a:tbn
[1] 4d98.b
-
0.3 0.1 0.1 0 0.6 0 0.6 0.2 0.1 0.2
[1] 4d9h.a -
0
0.1 0 0 0.5 0 0.2 0 0 0.1
[1] 4da0.a - 0.1
0
0 0 0.4 0 0.2 0.2 0 0.2
[1] 4da6.a - 0.1 0.1
0
0 0.6 0 0.3 0.1 0 0.1
[1] 4da7.a - 0 0.1 0
0
0.5 0 0.3 0 0 0.1
[1] 4da8.a - 0.1 0.1 0 0
0.2
0 0.2 0.1 0 0.1
[1] 4dab.a - 0 0.1 0 0 0.4
0
0.3 0 0 0.1
[1] 4dae.a - 0 0.1 0.1 0 0.4 0
0.2
0.1 0 0.2
[1] 4dan.a - 0.1 0.1 0 0 0.4 0 0.3
0.1
0 0.2
[1] 4dao.a - 0.2 0.2 0.1 0 0.8 0 0.5 0.1
0
0.2
[1] 4dar.a - 0 0 0 0 0.3 0 0.2 0 0
0
[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
4d98.b
4d9h.a
4da0.a
4da6.a
4da7.a
4da8.a
4dab.a
4dae.a
4dan.a
4dao.a
4dar.a
[1] 4d98.b
0
.04 .05 .03 .03 .06 .04 .04 .03 .05 .05
[1] 4d9h.a .04
0
.03 .01 .01 .03 .01 .01 .02 .02 .02
[1] 4da0.a .05 .03
0
.03 .03 .03 .02 .02 .03 .04 .01
[1] 4da6.a .03 .01 .03
0
0 .03 .01 .02 .03 .03 .01
[1] 4da7.a .03 .01 .03 0
0
.03 .01 .02 .03 .03 .01
[1] 4da8.a .06 .03 .03 .03 .03
0
.02 .03 .04 .05 .01
[1] 4dab.a .04 .01 .02 .01 .01 .02
0
.01 .02 .03 .01
[1] 4dae.a .04 .01 .02 .02 .02 .03 .01
0
.01 .02 .02
[1] 4dan.a .03 .02 .03 .03 .03 .04 .02 .01
0
.03 .03
[1] 4dao.a .05 .02 .04 .03 .03 .05 .03 .02 .03
0
.04
[1] 4dar.a .05 .02 .01 .01 .01 .01 .01 .02 .03 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
4d98.b
4d9h.a
4da0.a
4da6.a
4da7.a
4da8.a
4dab.a
4dae.a
4dan.a
4dao.a
4dar.a
[1] 4d98.b
0
1.8 1.8 1.8 1.8 1.8 1.8 1.7 1.8 1.8 1.8
[1] 4d9h.a 1.8
0
0.3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
[1] 4da0.a 1.8 0.3
0
0.2 0.3 0.2 0.3 0.2 0.2 0.3 0.3
[1] 4da6.a 1.8 0.2 0.2
0
0.1 0.2 0.2 0.2 0.2 0.3 0.3
[1] 4da7.a 1.8 0.2 0.3 0.1
0
0.2 0.1 0.2 0.3 0.3 0.3
[1] 4da8.a 1.8 0.2 0.2 0.2 0.2
0
0.2 0.2 0.2 0.3 0.2
[1] 4dab.a 1.8 0.2 0.3 0.2 0.1 0.2
0
0.2 0.3 0.3 0.2
[1] 4dae.a 1.7 0.2 0.2 0.2 0.2 0.2 0.2
0
0.2 0.3 0.3
[1] 4dan.a 1.8 0.2 0.2 0.2 0.3 0.2 0.3 0.2
0
0.3 0.3
[1] 4dao.a 1.8 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3
0
0.3
[1] 4dar.a 1.8 0.2 0.3 0.3 0.3 0.2 0.2 0.3 0.3 0.3
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
4d98.b
4d9h.a
4da0.a
4da6.a
4da7.a
4da8.a
4dab.a
4dae.a
4dan.a
4dao.a
4dar.a
[1] 4d98.b
0
2.0 2.1 2.0 1.8 2.0 1.9 2.0 2.0 2.1 2.0
[1] 4d9h.a 2.0
0
0.7 0.3 0.5 0.3 0.4 0.4 0.3 0.9 0.3
[1] 4da0.a 2.1 0.7
0
0.7 0.8 0.7 0.8 0.7 0.7 1.1 0.7
[1] 4da6.a 2.0 0.3 0.7
0
0.5 0.3 0.5 0.3 0.3 0.9 0.4
[1] 4da7.a 1.8 0.5 0.8 0.5
0
0.6 0.5 0.6 0.5 1.1 0.6
[1] 4da8.a 2.0 0.3 0.7 0.3 0.6
0
0.4 0.4 0.3 0.9 0.3
[1] 4dab.a 1.9 0.4 0.8 0.5 0.5 0.4
0
0.6 0.5 1.0 0.4
[1] 4dae.a 2.0 0.4 0.7 0.3 0.6 0.4 0.6
0
0.4 0.9 0.4
[1] 4dan.a 2.0 0.3 0.7 0.3 0.5 0.3 0.5 0.4
0
0.9 0.3
[1] 4dao.a 2.1 0.9 1.1 0.9 1.1 0.9 1.0 0.9 0.9
0
0.9
[1] 4dar.a 2.0 0.3 0.7 0.4 0.6 0.3 0.4 0.4 0.3 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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