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DCYD_SALTY_1_328

D-cysteine desulfhydrase [ACC deaminase/D-cysteine desulfhydrase family]

Composition of the binding site

Protein chains monomer
A1 (DCYD_SALTY):50, 51, 54, 73:75, 78:80, 158, 159, 161, 192:198, 261, 287, 315:31750, 51, 54, 73:75, 78:80, 158, 159, 161, 192:198, 261, 287, 315:317

Full PDB list

4d8t, 4d8u, 4d8w, 4d92, 4d96, 4d97, 4d99, 4d9b, 4d9c, 4d9e, 4d9f (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
N
5
0
K
5
1
K
5
4
A
7
3
G
7
4
A
7
5
S
7
8
N
7
9
H
8
0
V
1
5
8
G
1
5
9
A
1
9
2
G
1
9
4
S
1
9
5
A
1
9
6
G
1
9
7
T
1
9
8
Y
2
6
1
Y
2
8
7
T
3
1
5
G
3
1
6
G
3
1
7
[1]4d96.a 5pa22 . . . . . . . . . . . . . . . . . . . . . .
[1]4d9b.a pmp16 . . . . . . . . . . . . . . . . . . . . . .
[1]4d9e.d lcs22 . . . . . . . . . . . . . . . . . . . . . .
[1]4d9f.a dcs22 . . . . . . . . . . . . . . . . . . . . . .
[2]4d8w.d none . * . . . . . . . . . . . . . . . . . . . .
[2]4d97.a dsn7 . * . . . . . . . . . . . . . . . . . . . .
[2]4d99.a S7 . * . . . . . . . . . . . . . . . . . . . .

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
N
5
0
K
5
1
K
5
4
A
7
3
G
7
4
A
7
5
S
7
8
N
7
9
H
8
0
V
1
5
8
G
1
5
9
S
1
6
1
A
1
9
2
S
1
9
3
G
1
9
4
S
1
9
5
A
1
9
6
G
1
9
7
T
1
9
8
Y
2
6
1
Y
2
8
7
T
3
1
5
G
3
1
6
G
3
1
7
[1]4d96.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]4d9b.a . . . . . . . . . . . . . . . . . . . . . . . .
[1]4d9e.d . . . . . . . . . . . . . . . . . . . . . . . .
[1]4d9f.a . . . . . . . . . . . . . . . . . . . . . . . .
[2]4d8w.d . it1 . . . . . . . . . . . . . . . . . . . . . .
[2]4d97.a . it1 . . . . . . . . . . . . . . . . . . . . . .
[2]4d99.a . it1 . . . . . . . . . . . . . . . . . . . . . .

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
4d96.a:5pa
4d9b.a:pmp
4d9e.d:lcs
4d9f.a:dcs
4d8w.d is apo
4d97.a:dsn
4d99.a:S
[1] 4d96.a
0.2
0.1 0 0.4 - 0.1 0
[1] 4d9b.a 0.3
0.1
0 0.4 - 0.2 0
[1] 4d9e.d 0.3 0.1
0.1
0.4 - 0.2 0.1
[1] 4d9f.a 0.3 0.4 0.2
0.2
- 0.2 0.1
[2] 4d8w.d 12 13 12 12
-
0.2 0
[2] 4d97.a 13 14 12 12 -
0.2
0
[2] 4d99.a 13 14 12 12 - 0.2
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
4d96.a
4d9b.a
4d9e.d
4d9f.a
4d8w.d
4d97.a
4d99.a
[1] 4d96.a
0
0 0 .02 .57 .58 .57
[1] 4d9b.a 0
0
0 .03 .56 .57 .57
[1] 4d9e.d 0 0
0
.02 .57 .58 .57
[1] 4d9f.a .02 .03 .02
0
.56 .56 .56
[2] 4d8w.d .57 .56 .57 .56
0
.02 .01
[2] 4d97.a .58 .57 .58 .56 .02
0
.01
[2] 4d99.a .57 .57 .57 .56 .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
4d96.a
4d9b.a
4d9e.d
4d9f.a
4d8w.d
4d97.a
4d99.a
[1] 4d96.a
0
0.2 0.2 0.2 0.2 0.2 0.2
[1] 4d9b.a 0.2
0
0.1 0.2 0.2 0.2 0.2
[1] 4d9e.d 0.2 0.1
0
0.2 0.2 0.2 0.2
[1] 4d9f.a 0.2 0.2 0.2
0
0.2 0.2 0.2
[2] 4d8w.d 0.2 0.2 0.2 0.2
0
0.1 0.1
[2] 4d97.a 0.2 0.2 0.2 0.2 0.1
0
0.1
[2] 4d99.a 0.2 0.2 0.2 0.2 0.1 0.1
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
4d96.a
4d9b.a
4d9e.d
4d9f.a
4d8w.d
4d97.a
4d99.a
[1] 4d96.a
0
0.4 0.4 0.3 0.4 0.4 0.5
[1] 4d9b.a 0.4
0
0.3 0.5 0.6 0.6 0.5
[1] 4d9e.d 0.4 0.3
0
0.4 0.5 0.5 0.4
[1] 4d9f.a 0.3 0.5 0.4
0
0.3 0.3 0.4
[2] 4d8w.d 0.4 0.6 0.5 0.3
0
0.3 0.4
[2] 4d97.a 0.4 0.6 0.5 0.3 0.3
0
0.3
[2] 4d99.a 0.5 0.5 0.4 0.4 0.4 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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