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CCPA_BACME_53_332

Catabolite control protein A

Composition of the binding site

Protein chains monomer
A1 (CCPA_BACME):85, 88, 89, 157, 295, 296, 299:301, 303, 304, 307, 314, 319, 32185, 88, 89, 157, 295, 296, 299:301, 303, 304, 307, 314, 319, 321

Full PDB list

1rzr, 1sxg, 1sxh, 1sxi, 1zvv, 2hsg, 2jcg, 2nzu, 2nzv, 2oen (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
I
8
5
M
8
8
Y
8
9
D
2
9
6
A
2
9
9
V
3
0
0
R
3
0
3
L
3
0
4
K
3
0
7
V
3
1
9
[1]1rzr.a IM16 . * . . . . . . . .
[1]1rzr.c sepIMGV37 . * . . . . . . . .
[1]1zvv.a IM16 . . . . . . . . . .
[1]1zvv.b IMGLM36 . . . . . . . . . .
[1]2oen.g sepIM26 . . . . . . . . . .
[2]1sxg.a 17113 . . . . . . . . . .
[2]1sxi.d none . * . . . . . . . .
[2]2hsg.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

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PDB.ch
A1
I
8
5
M
8
8
Y
8
9
V
1
5
7
Y
2
9
5
D
2
9
6
A
2
9
9
V
3
0
0
A
3
0
1
R
3
0
3
L
3
0
4
K
3
0
7
V
3
1
4
V
3
1
9
L
3
2
1
[1]1rzr.a . * . . . . . . . . . . . . .
[1]1rzr.c . * . . . . . . . . . . . . .
[1]1zvv.a . . . . . . . . . . . . . . .
[1]1zvv.b . . . . . . . . . . . . . . .
[1]2oen.g . . . . . . . . . . . . . . .
[2]1sxg.a . . . . . . * . . * . . . . .
[2]1sxi.d . * . . * . . * . * . . . . .
[2]2hsg.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
1rzr.a:IM
1rzr.c:sepIMGV
1zvv.a:IM
1zvv.b:IMGLM
2oen.g:sepIM
1sxg.a:171
1sxi.d is apo
2hsg.a is apo
[1] 1rzr.a
0
0 0 0.4 0 0.3 - -
[1] 1rzr.c 0.1
0.1
0.1 0.4 0.1 0.4 - -
[1] 1zvv.a 0.1 0
0.1
0.1 0.1 0.1 - -
[1] 1zvv.b 0 0.1 0
0
0 0.4 - -
[1] 2oen.g 0.4 0.5 0.2 0.2
0
0.3 - -
[2] 1sxg.a 2.0 3.3 2.2 2.6 2.4
0
- -
[2] 1sxi.d 2.2 2.7 1.6 3.6 2.9 0.8
-
-
[2] 2hsg.a 1.9 2.0 2.0 2.5 1.1 1.4 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
1rzr.a
1rzr.c
1zvv.a
1zvv.b
2oen.g
1sxg.a
1sxi.d
2hsg.a
[1] 1rzr.a
0
.04 .03 .04 .07 .33 .34 .19
[1] 1rzr.c .04
0
.05 .05 .08 .33 .31 .19
[1] 1zvv.a .03 .05
0
.03 .06 .30 .32 .19
[1] 1zvv.b .04 .05 .03
0
.07 .31 .31 .17
[1] 2oen.g .07 .08 .06 .07
0
.32 .33 .21
[2] 1sxg.a .33 .33 .30 .31 .32
0
.23 .15
[2] 1sxi.d .34 .31 .32 .31 .33 .23
0
.25
[2] 2hsg.a .19 .19 .19 .17 .21 .15 .25
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
1rzr.a
1rzr.c
1zvv.a
1zvv.b
2oen.g
1sxg.a
1sxi.d
2hsg.a
[1] 1rzr.a
0
0.6 0.8 1.0 0.8 2.2 2.0 1.2
[1] 1rzr.c 0.6
0
0.7 1.0 0.9 2.1 2.0 1.3
[1] 1zvv.a 0.8 0.7
0
0.9 0.8 2.2 2.0 1.2
[1] 1zvv.b 1.0 1.0 0.9
0
1.1 1.7 1.5 0.8
[1] 2oen.g 0.8 0.9 0.8 1.1
0
2.2 2.0 1.4
[2] 1sxg.a 2.2 2.1 2.2 1.7 2.2
0
0.5 1.4
[2] 1sxi.d 2.0 2.0 2.0 1.5 2.0 0.5
0
1.3
[2] 2hsg.a 1.2 1.3 1.2 0.8 1.4 1.4 1.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.2 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
1rzr.a
1rzr.c
1zvv.a
1zvv.b
2oen.g
1sxg.a
1sxi.d
2hsg.a
[1] 1rzr.a
0
0.9 1.1 1.3 1.3 2.6 2.6 1.8
[1] 1rzr.c 0.9
0
1.1 1.3 1.1 2.5 2.5 1.7
[1] 1zvv.a 1.1 1.1
0
0.9 1.1 2.3 2.4 1.8
[1] 1zvv.b 1.3 1.3 0.9
0
1.3 2.1 2.1 1.7
[1] 2oen.g 1.3 1.1 1.1 1.3
0
2.5 2.5 1.8
[2] 1sxg.a 2.6 2.5 2.3 2.1 2.5
0
1.6 2.0
[2] 1sxi.d 2.6 2.5 2.4 2.1 2.5 1.6
0
1.9
[2] 2hsg.a 1.8 1.7 1.8 1.7 1.8 2.0 1.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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