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DODEC_HALS3_1_67

Dodecin [Dodecin family]

Composition of the binding site

Protein chains homotetramer
A1 (DODEC_HALS3):3, 33, 35:38, 633, 33, 35:38, 63
A2 (DODEC_HALS3):43:49, 5543:49, 55
A3 (DODEC_HALS3):45, 48, 5545, 48, 55
A4 (DODEC_HALS3):3, 36, 383, 36, 38
Metals (Me):Mg/Na

Full PDB list

1mog, 2cc6, 2cc7, 2cc8, 2cc9, 2ccb, 2ccc, 2cie, 2cif, 2cjc, 2vkf, 2vkg, 2vx9, 4b2h, 4b2j, 4b2k, 4b2m (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 A3 A4 Me
F
3
N
3
3
V
3
5
W
3
6
A
3
7
E
3
8
E
6
3
G
4
3
V
4
4
E
4
5
I
4
6
G
4
7
A
4
8
Q
5
5
E
4
5
A
4
8
Q
5
5
F
3
W
3
6
[1]1mog.a rbf27 . . . . . . . . . . . . . . . . . . . Mg
[1]2cc7.a lum18 . . . . . . . . . . . . . . . . . . . Mg
[1]2cc9.a none . . . . . . . . . . . . . . . . . . . Mg
[1]2ccc.a lfn19 . . . . . . . . . . . . . . . . . . . Mg
[1]2cjc.a fad38 . . . . . . . . . . . . . . . . . . . Mg
[1]2vx9.a rbf27 . . . . . . . . . A . . . . A . . . . Na
[1]4b2j.a rbf18 . . . * . . . . . . . . . . . . . . * Mg
[1]4b2k.a rbf18 . . . * . . . . . . . . . . . . . . * Mg
[1]4b2m.a rbf18 . . . * . . . . . . . . . . . . . . * Mg
[2]2vkf.a cf242 . . . . . . . . . A . . . . A . . - - Mg
[2]2vkg.a cf426 . . . . . . . . . A . . . . A . . - - Mg
[2]4b2h.a c3f25 . . . . . . . . . A . . . . A . . - - Na

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 A3 A4 Me
F
3
N
3
3
V
3
5
W
3
6
A
3
7
E
3
8
E
6
3
G
4
3
V
4
4
E
4
5
I
4
6
G
4
7
A
4
8
V
4
9
Q
5
5
E
4
5
A
4
8
Q
5
5
F
3
W
3
6
E
3
8
[1]1mog.a . . . . . . . . . * . * * . . . . . . . . Mg
[1]2cc7.a . . . . . . . . . * . * * . . . . . . . . Mg
[1]2cc9.a . . . . . . . . . * . * * . . . . . . . . Mg
[1]2ccc.a . . . . . . . . . * . * * . . . . . . . . Mg
[1]2cjc.a . . . . . . . . . * . * * . . . . . . . . Mg
[1]2vx9.a . . . . . . . . . A . * * . . A . . . . . Na
[1]4b2j.a . . . * . . . . . . . * * . . . . . . * . Mg
[1]4b2k.a . . . * . . . . . . . * * . . . . . . * . Mg
[1]4b2m.a . . . * . . . . . . . * * . . . . . . * . Mg
[2]2vkf.a . . . . . . . . . A . . . . . A . . - - - Mg
[2]2vkg.a . . . . . . . . . A . . . . . A . . - - - Mg
[2]4b2h.a . . . . . . . . . A . . . . . A . . - - - Na

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
1mog.a:rbf
2cc7.a:lum
2cc9.a is apo
2ccc.a:lfn
2cjc.a:fad
2vx9.a:rbf
4b2j.a:rbf
4b2k.a:rbf
4b2m.a:rbf
2vkf.a:cf2
2vkg.a:cf4
4b2h.a:c3f
[1] 1mog.a
0
0 - 0 0.2 0.1 0 0 0 5.6 4.0 2.7
[1] 2cc7.a 0
0
- 0 0.2 0.1 0 0 0.1 6.1 3.1 2.2
[1] 2cc9.a 0.3 0.2
-
0.2 0.4 0.2 0.2 0.2 0.3 6.4 3.9 2.9
[1] 2ccc.a 0.1 0 -
0
0.1 0 0 0 0 6.0 3.5 2.0
[1] 2cjc.a 0.4 0.1 - 0.1
0.3
0.3 0.1 0 0.1 5.3 4.3 2.8
[1] 2vx9.a 0 0 - 0 0.1
0
0 0 0 4.3 2.4 1.2
[1] 4b2j.a 0.2 0 - 0.1 0.4 0.2
0
0 0.2 4.9 2.8 1.7
[1] 4b2k.a 0.5 0.1 - 0.1 0.6 0.6 0.1
0
0.1 5.0 3.2 2.2
[1] 4b2m.a 0.1 0 - 0.1 0.2 0.1 0 0
0.1
4.2 2.9 1.4
[2] 2vkf.a 0 0 - 0 0.3 0.1 0 0 0
0.1
0 0.1
[2] 2vkg.a 0 0 - 0 0.2 0 0 0 0 0.1
0
0
[2] 4b2h.a 0 0 - 0 0.1 0 0 0 0 0.4 0
0
[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
1mog.a
2cc7.a
2cc9.a
2ccc.a
2cjc.a
2vx9.a
4b2j.a
4b2k.a
4b2m.a
2vkf.a
2vkg.a
4b2h.a
[1] 1mog.a
0
.06 .06 .05 .07 .09 .07 .12 .09 .27 .27 .27
[1] 2cc7.a .06
0
.05 .05 .08 .08 .10 .09 .13 .30 .29 .27
[1] 2cc9.a .06 .05
0
.05 .04 .10 .10 .10 .13 .30 .30 .30
[1] 2ccc.a .05 .05 .05
0
.05 .09 .09 .13 .12 .30 .30 .28
[1] 2cjc.a .07 .08 .04 .05
0
.11 .10 .12 .14 .30 .31 .31
[1] 2vx9.a .09 .08 .10 .09 .11
0
.06 .08 .08 .21 .21 .20
[1] 4b2j.a .07 .10 .10 .09 .10 .06
0
.06 .06 .25 .25 .25
[1] 4b2k.a .12 .09 .10 .13 .12 .08 .06
0
.10 .27 .28 .28
[1] 4b2m.a .09 .13 .13 .12 .14 .08 .06 .10
0
.22 .22 .22
[2] 2vkf.a .27 .30 .30 .30 .30 .21 .25 .27 .22
0
0 .02
[2] 2vkg.a .27 .29 .30 .30 .31 .21 .25 .28 .22 0
0
.02
[2] 4b2h.a .27 .27 .30 .28 .31 .20 .25 .28 .22 .02 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
1mog.a
2cc7.a
2cc9.a
2ccc.a
2cjc.a
2vx9.a
4b2j.a
4b2k.a
4b2m.a
2vkf.a
2vkg.a
4b2h.a
[1] 1mog.a
0
0.3 0.3 0.5 0.6 0.5 0.4 0.5 0.4 2.8 2.7 2.6
[1] 2cc7.a 0.3
0
0.2 0.3 0.4 0.3 0.3 0.3 0.4 2.9 2.8 2.7
[1] 2cc9.a 0.3 0.2
0
0.3 0.4 0.4 0.2 0.3 0.4 2.9 2.8 2.7
[1] 2ccc.a 0.5 0.3 0.3
0
0.2 0.1 0.2 0.3 0.2 2.9 2.8 2.7
[1] 2cjc.a 0.6 0.4 0.4 0.2
0
0.3 0.3 0.3 0.4 3.0 2.9 2.8
[1] 2vx9.a 0.5 0.3 0.4 0.1 0.3
0
0.3 0.4 0.2 2.8 2.8 2.6
[1] 4b2j.a 0.4 0.3 0.2 0.2 0.3 0.3
0
0.3 0.2 2.8 2.8 2.6
[1] 4b2k.a 0.5 0.3 0.3 0.3 0.3 0.4 0.3
0
0.4 3.0 3.0 2.8
[1] 4b2m.a 0.4 0.4 0.4 0.2 0.4 0.2 0.2 0.4
0
2.8 2.7 2.6
[2] 2vkf.a 2.8 2.9 2.9 2.9 3.0 2.8 2.8 3.0 2.8
0
0.1 0.3
[2] 2vkg.a 2.7 2.8 2.8 2.8 2.9 2.8 2.8 3.0 2.7 0.1
0
0.2
[2] 4b2h.a 2.6 2.7 2.7 2.7 2.8 2.6 2.6 2.8 2.6 0.3 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1mog.a
2cc7.a
2cc9.a
2ccc.a
2cjc.a
2vx9.a
4b2j.a
4b2k.a
4b2m.a
2vkf.a
2vkg.a
4b2h.a
[1] 1mog.a
0
0.3 0.3 0.4 0.5 0.4 0.8 0.9 0.9 2.4 2.4 2.3
[1] 2cc7.a 0.3
0
0.3 0.3 0.4 0.4 0.8 0.8 0.9 2.5 2.5 2.5
[1] 2cc9.a 0.3 0.3
0
0.3 0.4 0.4 0.8 0.9 0.9 2.5 2.5 2.4
[1] 2ccc.a 0.4 0.3 0.3
0
0.2 0.3 0.8 0.9 0.9 2.5 2.5 2.4
[1] 2cjc.a 0.5 0.4 0.4 0.2
0
0.4 0.9 0.9 0.9 2.6 2.6 2.5
[1] 2vx9.a 0.4 0.4 0.4 0.3 0.4
0
0.6 0.7 0.6 2.5 2.5 2.4
[1] 4b2j.a 0.8 0.8 0.8 0.8 0.9 0.6
0
0.2 0.2 2.5 2.5 2.4
[1] 4b2k.a 0.9 0.8 0.9 0.9 0.9 0.7 0.2
0
0.3 2.7 2.6 2.5
[1] 4b2m.a 0.9 0.9 0.9 0.9 0.9 0.6 0.2 0.3
0
2.5 2.5 2.4
[2] 2vkf.a 2.4 2.5 2.5 2.5 2.6 2.5 2.5 2.7 2.5
0
0.1 0.5
[2] 2vkg.a 2.4 2.5 2.5 2.5 2.6 2.5 2.5 2.6 2.5 0.1
0
0.5
[2] 4b2h.a 2.3 2.5 2.4 2.4 2.5 2.4 2.4 2.5 2.4 0.5 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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