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CHTB_VIBCH_22_124

Cholera enterotoxin subunit B

Composition of the binding site

Protein chains homodimer
A1 (CHTB_VIBCH):32:35, 72, 76:79, 82, 109, 111, 11232:35, 72, 76:79, 82, 109, 111, 112
A2 (CHTB_VIBCH):53:5653:56

Full PDB list

1chp, 1chq, 1ct1, 1eei, 1fgb, 1g8z, 1jr0, 1llr, 1md2, 1pzj, 1pzk, 1rcv, 1rd9, 1rdp, 1rf2, 1s5b, 1s5c, 1s5d, 1s5e, 1s5f, 1xtc, 2chb, 3chb, 3efx, 5elb, 5elc, 5eld, 5ele, 5elf, 5lzg, 5lzh, 5lzj (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
E
3
2
Y
3
3
H
3
4
N
3
5
E
7
2
S
7
6
Q
7
7
H
7
8
I
7
9
Q
8
2
W
1
0
9
N
1
1
1
K
1
1
2
G
5
4
K
5
5
R
5
6
[1]1chp.e none . . . . . . . . . . . . . D . .
[1]1chq.e none . . . . . . . . . . . . . . . D
[1]1ct1.f none . . . . . . . . . . . . . R . .
[1]1eei.e gaa21 . . . . . . . . . . . . . . . .
[1]1g8z.d none . . . . . . . A . . . . . . . .
[1]1jr0.d a2432 . . . . . . . . . . . . . . . .
[1]1llr.f fng.lnq37 . . . . . . . . . . . . . . . .
[1]1md2.d 233,233.sq84 . . . . . . . . . . . . . . . .
[1]1md2.f cyn.23326 . . . . . . . . . . . . . . . .
[1]1pzj.d 15b37 . . . . . . . . . . . . . . . .
[1]1pzj.f j1537 . . . . . . . . . . . . . . . .
[1]1pzk.d j1221 . . . . . . . . . . . . . . . .
[1]1rcv.d bv124 . . . . . . . . . . . . . . . .
[1]1rd9.d bv224 . . . . . . . . . . . . . . . .
[1]1rdp.d bv324 . . . . . . . . . . . . . . . .
[1]1rf2.d bv424 . . . . . . . . . . . . . . . .
[1]3chb.e none . . . . . . . . . . . . . . . .
[1]5elb.a gla12 . . . . . . . . . . . . . . . .
[1]5lzg.a 7bn43 . . . . . . . . . . . . . . . .
[1]5lzh.a 7bo43 . . . . . . . . . . . . . . . .
[1]5lzj.c 7bt30 . . . . . . . . . . . . . . . .

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 A2
E
3
2
Y
3
3
H
3
4
N
3
5
E
7
2
S
7
6
Q
7
7
H
7
8
I
7
9
Q
8
2
W
1
0
9
N
1
1
1
K
1
1
2
A
5
3
G
5
4
K
5
5
R
5
6
[1]1chp.e . . . . . . . . . . . . . . D . .
[1]1chq.e . . . . . . . . . . . . . . . . D
[1]1ct1.f . . . . . . . . . . . . . . R . .
[1]1eei.e . . . . . . . . . . . . . . . . .
[1]1g8z.d . . . . . . . A . . . . . . . * .
[1]1jr0.d . . . . . . . . . . . . . . . . .
[1]1llr.f . . . . . . . . . . . . . . . . .
[1]1md2.d . . . . . . . . . . . . . . . . .
[1]1md2.f . . . . . . . . . . . . . . . . .
[1]1pzj.d . . . . . . . . . . . . . . . . .
[1]1pzj.f . . . . . . . . . . . . . . . . .
[1]1pzk.d . . . . . . . . . . . . . . . . .
[1]1rcv.d . . . . . . . . . . . . . . . . .
[1]1rd9.d . . . . . . . . . . . . . . . . .
[1]1rdp.d . . . . . . . . . . . . . . . . .
[1]1rf2.d . . . . . . . . . . . . . . . . .
[1]3chb.e . . . . . . . . . . . . . . . . .
[1]5elb.a . . . . . . . . . . . . . . . . .
[1]5lzg.a . . . . . . . . . . . . . . . . .
[1]5lzh.a . . . . . . . . . . . . . . . . .
[1]5lzj.c . . . . . . . . . . . . . . . . .

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
1chp.e is apo
1chq.e is apo
1ct1.f is apo
1eei.e:gaa
1g8z.d is apo
1jr0.d:a24
1llr.f:fng.lnq
1md2.d:233,233.sq
1md2.f:cyn.233
1pzj.d:15b
1pzj.f:j15
1pzk.d:j12
1rcv.d:bv1
1rd9.d:bv2
1rdp.d:bv3
1rf2.d:bv4
3chb.e is apo
5elb.a:gla
5lzg.a:7bn
5lzh.a:7bo
5lzj.c:7bt
[1] 1chp.e
-
- - 0.3 - 1.1 0.6 0.1 0.1 0.4 0.6 0.1 0.3 0.3 0.5 0.5 - 0 0.9 0.9 0.1
[1] 1chq.e -
-
- 0.3 - 0.4 0.3 0.4 0.4 0.4 0.5 0.4 0.3 0.4 0.6 0.6 - 0.2 0.5 0.6 0.4
[1] 1ct1.f - -
-
0.1 - 2.2 0.2 1.5 0.1 0.1 0.3 0.1 0.2 0.1 0.2 0.2 - 0 0.5 0.6 0.1
[1] 1eei.e - - -
0
- 0 0 0 0 0 0 0 0 0 0 0 - 0 0 0 0
[1] 1g8z.d - - - 0
-
0.1 0.9 0 0 0.6 0.1 0 0 0 0 0 - 0 0 0 0
[1] 1jr0.d - - - 0 -
0
0.1 0 0.1 0.1 0.1 0 0.1 0.1 0.1 0.1 - 0 0 0 0.3
[1] 1llr.f - - - 0 - 0
0
0 0 0 0 0 0 0 0 0 - 0 0 0 0.1
[1] 1md2.d - - - 0 - 0 0
0
0.1 0.1 0.1 0 0 0 0 0 - 0 0 0 0.2
[1] 1md2.f - - - 0 - 0 0.1 0
0
0.1 0.1 0 0 0 0 0 - 0 0 0 0
[1] 1pzj.d - - - 0 - 0.1 0 0.1 0
0
0 0 0 0 0 0 - 0 0 0 0
[1] 1pzj.f - - - 0 - 0 0 0 0 0
0
0 0 0 0 0 - 0 0 0 0
[1] 1pzk.d - - - 0.1 - 0 0 0 0.1 0.2 0.1
0
0 0 0 0.1 - 0 0 0.1 0.1
[1] 1rcv.d - - - 0 - 0 0 0.1 0 0 0 0
0
0 0 0 - 0 0 0 0
[1] 1rd9.d - - - 0 - 0 0 0.1 0 0 0 0 0
0
0 0 - 0 0 0 0.1
[1] 1rdp.d - - - 0 - 0 0 0 0 0 0 0 0 0
0
0 - 0 0 0 0.1
[1] 1rf2.d - - - 0 - 0 0 0.1 0 0 0 0 0 0 0
0
- 0 0.1 0 0.1
[1] 3chb.e - - - 0.2 - 0 0.5 0 0.2 0.4 0.4 0 0.1 0 0.1 0.1
-
0 0 0 0.1
[1] 5elb.a - - - 0.1 - 0.1 0.1 0.1 0.1 0.1 0.1 0 0.1 0.1 0.1 0.1 -
0
0.1 0.1 0.1
[1] 5lzg.a - - - 0 - 0.1 0.5 0.1 0 0.3 0.3 0 0 0 0 0 - 0
0
0 0.1
[1] 5lzh.a - - - 0 - 0.1 0.4 0.1 0 0.4 0.6 0 0 0 0 0 - 0 0
0
0.2
[1] 5lzj.c - - - 0 - 0 0 0 0 0 0 0 0 0 0 0 - 0 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
1chp.e
1chq.e
1ct1.f
1eei.e
1g8z.d
1jr0.d
1llr.f
1md2.d
1md2.f
1pzj.d
1pzj.f
1pzk.d
1rcv.d
1rd9.d
1rdp.d
1rf2.d
3chb.e
5elb.a
5lzg.a
5lzh.a
5lzj.c
[1] 1chp.e
0
.09 .09 .07 .12 .09 .08 .08 .06 .08 .07 .07 .08 .08 .08 .08 .09 .06 .11 .11 .07
[1] 1chq.e .09
0
.17 .05 .11 .04 .04 .04 .05 .06 .05 .04 .04 .04 .04 .04 .06 .04 .08 .08 .05
[1] 1ct1.f .09 .17
0
.14 .18 .15 .14 .15 .14 .15 .14 .14 .14 .14 .14 .14 .17 .13 .18 .19 .14
[1] 1eei.e .07 .05 .14
0
.06 .02 .01 .01 .01 .01 0 .01 .01 .01 .01 .01 .05 .01 .05 .05 0
[1] 1g8z.d .12 .11 .18 .06
0
.08 .06 .07 .06 .07 .06 .07 .06 .06 .06 .06 .11 .06 .11 .11 .06
[1] 1jr0.d .09 .04 .15 .02 .08
0
.01 .01 .02 .03 .02 .02 .01 .01 .01 .01 .05 .02 .05 .05 .02
[1] 1llr.f .08 .04 .14 .01 .06 .01
0
.01 .01 .02 .01 .02 0 0 0 0 .05 .01 .04 .05 .01
[1] 1md2.d .08 .04 .15 .01 .07 .01 .01
0
.02 .02 .01 .01 .01 .01 .01 .01 .05 .02 .05 .04 .01
[1] 1md2.f .06 .05 .14 .01 .06 .02 .01 .02
0
.02 .01 .02 .01 .01 .01 .01 .04 .01 .04 .05 .01
[1] 1pzj.d .08 .06 .15 .01 .07 .03 .02 .02 .02
0
.01 .02 .02 .02 .02 .02 .06 .02 .04 .04 .01
[1] 1pzj.f .07 .05 .14 0 .06 .02 .01 .01 .01 .01
0
.01 .01 .01 .01 .01 .05 .01 .05 .05 0
[1] 1pzk.d .07 .04 .14 .01 .07 .02 .02 .01 .02 .02 .01
0
.02 .02 .02 .02 .04 .01 .06 .05 .01
[1] 1rcv.d .08 .04 .14 .01 .06 .01 0 .01 .01 .02 .01 .02
0
0 0 0 .05 .01 .04 .05 .01
[1] 1rd9.d .08 .04 .14 .01 .06 .01 0 .01 .01 .02 .01 .02 0
0
0 0 .05 .01 .04 .05 .01
[1] 1rdp.d .08 .04 .14 .01 .06 .01 0 .01 .01 .02 .01 .02 0 0
0
0 .05 .01 .04 .05 .01
[1] 1rf2.d .08 .04 .14 .01 .06 .01 0 .01 .01 .02 .01 .02 0 0 0
0
.05 .01 .04 .05 .01
[1] 3chb.e .09 .06 .17 .05 .11 .05 .05 .05 .04 .06 .05 .04 .05 .05 .05 .05
0
.04 .04 .03 .05
[1] 5elb.a .06 .04 .13 .01 .06 .02 .01 .02 .01 .02 .01 .01 .01 .01 .01 .01 .04
0
.05 .06 .01
[1] 5lzg.a .11 .08 .18 .05 .11 .05 .04 .05 .04 .04 .05 .06 .04 .04 .04 .04 .04 .05
0
.01 .05
[1] 5lzh.a .11 .08 .19 .05 .11 .05 .05 .04 .05 .04 .05 .05 .05 .05 .05 .05 .03 .06 .01
0
.05
[1] 5lzj.c .07 .05 .14 0 .06 .02 .01 .01 .01 .01 0 .01 .01 .01 .01 .01 .05 .01 .05 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1chp.e
1chq.e
1ct1.f
1eei.e
1g8z.d
1jr0.d
1llr.f
1md2.d
1md2.f
1pzj.d
1pzj.f
1pzk.d
1rcv.d
1rd9.d
1rdp.d
1rf2.d
3chb.e
5elb.a
5lzg.a
5lzh.a
5lzj.c
[1] 1chp.e
0
0.6 1.2 1.5 1.4 1.5 1.5 1.4 1.6 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.6 1.5 1.5 1.5
[1] 1chq.e 0.6
0
1.3 1.6 1.6 1.6 1.6 1.5 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.6 1.5 1.6 1.6 1.6 1.6
[1] 1ct1.f 1.2 1.3
0
0.5 2.5 0.4 0.5 0.4 0.5 0.5 0.5 0.5 0.5 0.5 0.4 0.4 0.5 0.5 0.5 0.5 0.5
[1] 1eei.e 1.5 1.6 0.5
0
2.8 0.2 0.2 0.2 0.2 0.3 0.2 0.2 0.3 0.3 0.2 0.2 0.3 0.2 0.3 0.3 0.2
[1] 1g8z.d 1.4 1.6 2.5 2.8
0
2.8 2.8 2.7 2.8 2.8 2.7 2.8 2.8 2.8 2.8 2.8 2.7 2.8 2.7 2.7 2.7
[1] 1jr0.d 1.5 1.6 0.4 0.2 2.8
0
0.2 0.2 0.2 0.2 0.2 0.1 0.1 0.1 0.1 0.1 0.2 0.2 0.3 0.3 0.2
[1] 1llr.f 1.5 1.6 0.5 0.2 2.8 0.2
0
0.1 0.2 0.1 0.1 0.2 0.2 0.2 0.2 0.1 0.2 0.2 0.2 0.2 0.2
[1] 1md2.d 1.4 1.5 0.4 0.2 2.7 0.2 0.1
0
0.2 0.2 0.1 0.2 0.2 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2
[1] 1md2.f 1.6 1.6 0.5 0.2 2.8 0.2 0.2 0.2
0
0.3 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.2 0.3 0.3 0.2
[1] 1pzj.d 1.5 1.6 0.5 0.3 2.8 0.2 0.1 0.2 0.3
0
0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
[1] 1pzj.f 1.5 1.6 0.5 0.2 2.7 0.2 0.1 0.1 0.2 0.1
0
0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
[1] 1pzk.d 1.5 1.6 0.5 0.2 2.8 0.1 0.2 0.2 0.2 0.2 0.2
0
0.1 0.1 0.1 0.1 0.2 0.1 0.3 0.3 0.2
[1] 1rcv.d 1.5 1.6 0.5 0.3 2.8 0.1 0.2 0.2 0.2 0.2 0.2 0.1
0
0.1 0.1 0.1 0.2 0.2 0.3 0.3 0.2
[1] 1rd9.d 1.5 1.6 0.5 0.3 2.8 0.1 0.2 0.1 0.2 0.2 0.2 0.1 0.1
0
0.1 0.1 0.2 0.2 0.3 0.3 0.2
[1] 1rdp.d 1.5 1.6 0.4 0.2 2.8 0.1 0.2 0.1 0.2 0.2 0.2 0.1 0.1 0.1
0
0.1 0.2 0.2 0.3 0.3 0.2
[1] 1rf2.d 1.5 1.6 0.4 0.2 2.8 0.1 0.1 0.1 0.2 0.2 0.2 0.1 0.1 0.1 0.1
0
0.2 0.2 0.2 0.2 0.2
[1] 3chb.e 1.5 1.5 0.5 0.3 2.7 0.2 0.2 0.2 0.3 0.2 0.2 0.2 0.2 0.2 0.2 0.2
0
0.2 0.2 0.2 0.2
[1] 5elb.a 1.6 1.6 0.5 0.2 2.8 0.2 0.2 0.2 0.2 0.2 0.2 0.1 0.2 0.2 0.2 0.2 0.2
0
0.3 0.3 0.2
[1] 5lzg.a 1.5 1.6 0.5 0.3 2.7 0.3 0.2 0.2 0.3 0.2 0.2 0.3 0.3 0.3 0.3 0.2 0.2 0.3
0
0.1 0.2
[1] 5lzh.a 1.5 1.6 0.5 0.3 2.7 0.3 0.2 0.2 0.3 0.2 0.2 0.3 0.3 0.3 0.3 0.2 0.2 0.3 0.1
0
0.2
[1] 5lzj.c 1.5 1.6 0.5 0.2 2.7 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1chp.e
1chq.e
1ct1.f
1eei.e
1g8z.d
1jr0.d
1llr.f
1md2.d
1md2.f
1pzj.d
1pzj.f
1pzk.d
1rcv.d
1rd9.d
1rdp.d
1rf2.d
3chb.e
5elb.a
5lzg.a
5lzh.a
5lzj.c
[1] 1chp.e
0
0.6 1.5 1.6 2.2 1.7 1.7 1.6 1.7 1.8 1.7 1.7 1.7 1.6 1.6 1.7 1.6 1.6 1.6 1.6 1.6
[1] 1chq.e 0.6
0
1.6 1.9 2.3 1.9 1.9 1.8 1.9 1.9 1.8 1.9 1.8 1.9 1.9 1.9 1.8 1.8 1.8 1.8 1.8
[1] 1ct1.f 1.5 1.6
0
0.8 2.7 0.9 1.0 1.0 0.7 1.0 0.7 1.0 0.7 0.8 0.8 0.7 0.8 0.8 0.8 0.8 0.8
[1] 1eei.e 1.6 1.9 0.8
0
3.0 0.7 0.8 0.8 0.5 0.8 0.6 0.8 0.5 0.4 0.6 0.4 0.4 0.6 0.6 0.6 0.5
[1] 1g8z.d 2.2 2.3 2.7 3.0
0
3.0 3.1 3.0 3.0 3.1 2.9 3.1 3.0 3.0 3.0 3.0 3.0 3.1 3.0 3.0 3.0
[1] 1jr0.d 1.7 1.9 0.9 0.7 3.0
0
0.7 0.6 0.8 0.3 0.8 0.3 0.7 0.7 0.6 0.7 0.7 0.7 0.7 0.8 0.7
[1] 1llr.f 1.7 1.9 1.0 0.8 3.1 0.7
0
0.7 0.8 0.6 0.9 0.6 0.8 0.9 0.9 0.9 0.9 0.8 0.9 0.8 0.8
[1] 1md2.d 1.6 1.8 1.0 0.8 3.0 0.6 0.7
0
1.0 0.5 1.0 0.5 0.9 0.9 0.9 0.9 0.9 0.9 0.9 1.0 0.9
[1] 1md2.f 1.7 1.9 0.7 0.5 3.0 0.8 0.8 1.0
0
0.9 0.4 0.9 0.3 0.5 0.7 0.5 0.5 0.5 0.6 0.6 0.5
[1] 1pzj.d 1.8 1.9 1.0 0.8 3.1 0.3 0.6 0.5 0.9
0
0.9 0.2 0.9 0.8 0.8 0.8 0.9 0.8 0.8 0.8 0.8
[1] 1pzj.f 1.7 1.8 0.7 0.6 2.9 0.8 0.9 1.0 0.4 0.9
0
0.9 0.4 0.5 0.7 0.5 0.6 0.6 0.7 0.7 0.6
[1] 1pzk.d 1.7 1.9 1.0 0.8 3.1 0.3 0.6 0.5 0.9 0.2 0.9
0
0.9 0.8 0.7 0.8 0.9 0.8 0.8 0.9 0.8
[1] 1rcv.d 1.7 1.8 0.7 0.5 3.0 0.7 0.8 0.9 0.3 0.9 0.4 0.9
0
0.3 0.6 0.4 0.5 0.5 0.6 0.6 0.5
[1] 1rd9.d 1.6 1.9 0.8 0.4 3.0 0.7 0.9 0.9 0.5 0.8 0.5 0.8 0.3
0
0.5 0.2 0.5 0.5 0.7 0.6 0.5
[1] 1rdp.d 1.6 1.9 0.8 0.6 3.0 0.6 0.9 0.9 0.7 0.8 0.7 0.7 0.6 0.5
0
0.5 0.6 0.5 0.5 0.6 0.6
[1] 1rf2.d 1.7 1.9 0.7 0.4 3.0 0.7 0.9 0.9 0.5 0.8 0.5 0.8 0.4 0.2 0.5
0
0.5 0.6 0.7 0.6 0.6
[1] 3chb.e 1.6 1.8 0.8 0.4 3.0 0.7 0.9 0.9 0.5 0.9 0.6 0.9 0.5 0.5 0.6 0.5
0
0.6 0.6 0.6 0.5
[1] 5elb.a 1.6 1.8 0.8 0.6 3.1 0.7 0.8 0.9 0.5 0.8 0.6 0.8 0.5 0.5 0.5 0.6 0.6
0
0.5 0.4 0.4
[1] 5lzg.a 1.6 1.8 0.8 0.6 3.0 0.7 0.9 0.9 0.6 0.8 0.7 0.8 0.6 0.7 0.5 0.7 0.6 0.5
0
0.3 0.5
[1] 5lzh.a 1.6 1.8 0.8 0.6 3.0 0.8 0.8 1.0 0.6 0.8 0.7 0.9 0.6 0.6 0.6 0.6 0.6 0.4 0.3
0
0.5
[1] 5lzj.c 1.6 1.8 0.8 0.5 3.0 0.7 0.8 0.9 0.5 0.8 0.6 0.8 0.5 0.5 0.6 0.6 0.5 0.4 0.5 0.5
0
[Binding site full-atom RMSD matrix]







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