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ARC3_CBDP_41_251

Mono-ADP-ribosyltransferase C3

Composition of the binding site

Protein chains monomer
A1 (ARC3_CBDP):80, 83, 84, 87, 91, 128:131, 133, 134, 167, 169, 174:176, 182, 183, 186, 209:212, 21480, 83, 84, 87, 91, 128:131, 133, 134, 167, 169, 174:176, 182, 183, 186, 209:212, 214

Full PDB list

1g24, 1gze, 1gzf, 1uzi, 2a78, 2a9k, 2bov, 2c89, 2c8a, 2c8b, 2c8c, 2c8d, 2c8e, 2c8f, 2c8g, 2c8h (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
8
0
A
8
3
S
8
4
N
8
7
R
9
1
R
1
2
8
G
1
2
9
D
1
3
0
D
1
3
1
A
1
3
3
Y
1
3
4
R
1
6
7
E
1
6
9
S
1
7
4
T
1
7
5
S
1
7
6
F
1
8
3
R
1
8
6
G
2
1
1
Q
2
1
2
E
2
1
4
[1]1g24.d none . . . . . . . . . . . . . . . . . . . . .
[1]1gzf.c adp,nir44 . . . . . . . . . . . . . . . . . . . . .
[1]1gzf.d adp27 . . . . . . . . . . . . . . . . . . . . .
[1]2a9k.b nad44 . . . . . . . . . . . . . . . . . . . . .
[1]2c8a.b nca9 . . . . . . . . . . . . . . . . . . . . .
[1]2c8c.b nad44 . . . . . . . . . . . . . . . . . . . A .
[1]2c8c.d adp27 . . . . . . . . . . . . . . . . . . . A .
[1]2c8d.a none . . . . . . . . . . . . . . . . . . . A .
[1]2c8e.e none . . . . . . . . . . . . . . . . . . . . N
[1]2c8f.e nad44 . . . . . . . . . . . . . . . . . . . . N
[1]2c8h.a nad44 . . . . . . . . . . . . . . . . . . . . .
[1]2c8h.c 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
T
8
0
A
8
3
S
8
4
N
8
7
R
9
1
R
1
2
8
G
1
2
9
D
1
3
0
D
1
3
1
A
1
3
3
Y
1
3
4
R
1
6
7
E
1
6
9
S
1
7
4
T
1
7
5
S
1
7
6
Q
1
8
2
F
1
8
3
R
1
8
6
F
2
0
9
A
2
1
0
G
2
1
1
Q
2
1
2
E
2
1
4
[1]1g24.d . . . . . . . . . . . . . . . . . . . . . . . .
[1]1gzf.c . . . . . . . . . . . . . . . . . . . . . . . .
[1]1gzf.d . . . . . . . . . . . . . . . . . . . . . . . .
[1]2a9k.b . . . . . . . . . . . . . . . . . . . . . . . .
[1]2c8a.b . . . . . . . . . . . . . . . . . . . . . . . .
[1]2c8c.b . . . . . . . . . . . . . . . . . . . . . . A .
[1]2c8c.d . . . . . . . . . . . . . . . . . . . . . . A .
[1]2c8d.a . . . . . . . . . . . . . . . . . . . . . . A .
[1]2c8e.e . . . . . . . . . . . . . . . . . . . . . . . N
[1]2c8f.e . . . . . . . . . . . . . . . . . . . . . . . N
[1]2c8h.a . . . . . . . . . . . . . . . . A . . . . . . .
[1]2c8h.c . . . . . . . . . . . . . . . . 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
1g24.d is apo
1gzf.c:adp,nir
1gzf.d:adp
2a9k.b:nad
2c8a.b:nca
2c8c.b:nad
2c8c.d:adp
2c8d.a is apo
2c8e.e is apo
2c8f.e:nad
2c8h.a:nad
2c8h.c is apo
[1] 1g24.d
-
0.7 0.3 0.3 0.2 0.2 0 - - 0.5 0.4 -
[1] 1gzf.c -
0
0.7 0.1 0 0 0.3 - - 0.1 0 -
[1] 1gzf.d - 1.1
0
0.7 0.7 0.4 0 - - 0.6 0.4 -
[1] 2a9k.b - 1.1 1.6
0.2
0 0.4 0.6 - - 0.5 0.1 -
[1] 2c8a.b - 0.3 1.1 0.3
0
0.2 0.3 - - 0.3 0.1 -
[1] 2c8c.b - 0.3 1.2 0.1 0
0
0.2 - - 0.1 0.1 -
[1] 2c8c.d - 0.9 0.2 0.8 0.6 0.4
0
- - 0.5 0.4 -
[1] 2c8d.a - 0.7 0.4 0.3 0.2 0.2 0.1
-
- 0.6 0.2 -
[1] 2c8e.e - 1.0 1.4 0.8 0.2 0.8 0.6 -
-
0.6 0.7 -
[1] 2c8f.e - 0.5 1.1 0 0 0.1 0.4 - -
0.2
0 -
[1] 2c8h.a - 0.6 1.3 0.1 0 0 0.4 - - 0.2
0.1
-
[1] 2c8h.c - 2.3 0.8 1.6 1.5 1.1 0.3 - - 1.4 1.3
-
[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
1g24.d
1gzf.c
1gzf.d
2a9k.b
2c8a.b
2c8c.b
2c8c.d
2c8d.a
2c8e.e
2c8f.e
2c8h.a
2c8h.c
[1] 1g24.d
0
.06 .03 .12 .08 .08 .02 .03 .08 .08 .09 .10
[1] 1gzf.c .06
0
.08 .08 .03 .03 .06 .05 .08 .05 .04 .10
[1] 1gzf.d .03 .08
0
.15 .09 .10 .03 .04 .10 .10 .11 .11
[1] 2a9k.b .12 .08 .15
0
.07 .05 .12 .12 .10 .05 .03 .16
[1] 2c8a.b .08 .03 .09 .07
0
.03 .08 .06 .09 .04 .04 .12
[1] 2c8c.b .08 .03 .10 .05 .03
0
.08 .08 .09 .02 .03 .12
[1] 2c8c.d .02 .06 .03 .12 .08 .08
0
.04 .10 .08 .10 .10
[1] 2c8d.a .03 .05 .04 .12 .06 .08 .04
0
.08 .07 .08 .10
[1] 2c8e.e .08 .08 .10 .10 .09 .09 .10 .08
0
.07 .09 .15
[1] 2c8f.e .08 .05 .10 .05 .04 .02 .08 .07 .07
0
.05 .13
[1] 2c8h.a .09 .04 .11 .03 .04 .03 .10 .08 .09 .05
0
.13
[1] 2c8h.c .10 .10 .11 .16 .12 .12 .10 .10 .15 .13 .13
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
1g24.d
1gzf.c
1gzf.d
2a9k.b
2c8a.b
2c8c.b
2c8c.d
2c8d.a
2c8e.e
2c8f.e
2c8h.a
2c8h.c
[1] 1g24.d
0
0.4 0.5 1.8 0.5 0.4 0.4 1.7 1.9 1.9 1.9 0.4
[1] 1gzf.c 0.4
0
0.6 1.8 0.5 0.4 0.5 1.8 1.9 1.9 1.9 0.3
[1] 1gzf.d 0.5 0.6
0
1.9 0.5 0.6 0.3 1.8 2.0 1.9 2.0 0.6
[1] 2a9k.b 1.8 1.8 1.9
0
1.7 1.7 1.8 0.9 0.7 0.6 0.8 1.7
[1] 2c8a.b 0.5 0.5 0.5 1.7
0
0.5 0.5 1.7 1.9 1.8 1.8 0.5
[1] 2c8c.b 0.4 0.4 0.6 1.7 0.5
0
0.6 1.7 1.9 1.9 1.9 0.4
[1] 2c8c.d 0.4 0.5 0.3 1.8 0.5 0.6
0
1.7 1.9 1.9 1.9 0.5
[1] 2c8d.a 1.7 1.8 1.8 0.9 1.7 1.7 1.7
0
1.0 1.0 0.6 1.7
[1] 2c8e.e 1.9 1.9 2.0 0.7 1.9 1.9 1.9 1.0
0
0.6 1.0 1.9
[1] 2c8f.e 1.9 1.9 1.9 0.6 1.8 1.9 1.9 1.0 0.6
0
1.0 1.9
[1] 2c8h.a 1.9 1.9 2.0 0.8 1.8 1.9 1.9 0.6 1.0 1.0
0
1.9
[1] 2c8h.c 0.4 0.3 0.6 1.7 0.5 0.4 0.5 1.7 1.9 1.9 1.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1g24.d
1gzf.c
1gzf.d
2a9k.b
2c8a.b
2c8c.b
2c8c.d
2c8d.a
2c8e.e
2c8f.e
2c8h.a
2c8h.c
[1] 1g24.d
0
1.2 0.8 2.3 1.2 1.2 0.7 1.7 2.1 2.3 2.4 0.8
[1] 1gzf.c 1.2
0
1.3 2.2 0.9 0.9 1.3 2.1 2.5 2.2 2.3 1.0
[1] 1gzf.d 0.8 1.3
0
2.5 1.4 1.4 0.4 1.9 2.3 2.5 2.5 0.8
[1] 2a9k.b 2.3 2.2 2.5
0
2.1 1.8 2.2 1.4 1.7 1.2 0.8 2.3
[1] 2c8a.b 1.2 0.9 1.4 2.1
0
0.8 1.4 1.9 2.4 2.1 2.2 1.1
[1] 2c8c.b 1.2 0.9 1.4 1.8 0.8
0
1.3 1.9 2.4 2.0 1.9 1.0
[1] 2c8c.d 0.7 1.3 0.4 2.2 1.4 1.3
0
1.9 2.2 2.3 2.2 0.8
[1] 2c8d.a 1.7 2.1 1.9 1.4 1.9 1.9 1.9
0
1.3 1.5 1.1 1.9
[1] 2c8e.e 2.1 2.5 2.3 1.7 2.4 2.4 2.2 1.3
0
1.7 1.6 2.3
[1] 2c8f.e 2.3 2.2 2.5 1.2 2.1 2.0 2.3 1.5 1.7
0
1.2 2.3
[1] 2c8h.a 2.4 2.3 2.5 0.8 2.2 1.9 2.2 1.1 1.6 1.2
0
2.4
[1] 2c8h.c 0.8 1.0 0.8 2.3 1.1 1.0 0.8 1.9 2.3 2.3 2.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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