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CYSK_MYCTU_2_310

O-acetylserine sulfhydrylase [Cysteine synthase/cystathionine beta- synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CYSK_MYCTU):R: Pyridoxal phosphate binding (178:182)
43, 44, 70:75, 95, 97, 98, 102, 117, 118, 120:123, 126, 144, 145, 176, 177, 215, 221:225, 227, 266, 293, 294, 299
43, 44, 70:75, 95, 97, 98, 102, 117, 118, 120:123, 126, 144, 145, 176:182, 215, 221:225, 227, 266, 293, 294, 299

Full PDB list

2q3b, 2q3c, 2q3d, 3zei

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
4
4
T
7
1
S
7
2
G
7
3
N
7
4
T
7
5
M
1
2
2
I
1
2
6
Q
1
4
4
F
1
4
5
V
1
7
7
G
1
7
8
T
1
7
9
G
1
8
0
T
1
8
2
K
2
1
5
Q
2
2
1
G
2
2
2
I
2
2
3
G
2
2
4
A
2
2
5
F
2
2
7
S
2
6
6
P
2
9
3
D
2
9
4
Y
2
9
9
[1]2q3b.a plp15 * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2q3c.a DFSI,plp49 * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zei.a awh,plp44 * . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2q3d.a pda21 . . . . . . . . . . . . . . . . . . . . . . . . . .

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
V
4
3
K
4
4
P
7
0
T
7
1
S
7
2
G
7
3
N
7
4
T
7
5
P
9
5
T
9
7
M
9
8
R
1
0
2
P
1
1
7
G
1
1
8
D
1
2
0
G
1
2
1
M
1
2
2
S
1
2
3
I
1
2
6
Q
1
4
4
F
1
4
5
G
1
7
6
V
1
7
7
G
1
7
8
T
1
7
9
G
1
8
0
G
1
8
1
T
1
8
2
K
2
1
5
Q
2
2
1
G
2
2
2
I
2
2
3
G
2
2
4
A
2
2
5
F
2
2
7
S
2
6
6
P
2
9
3
D
2
9
4
Y
2
9
9
[1]2q3b.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2q3c.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zei.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2q3d.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
2q3b.a:plp
2q3c.a:DFSI,plp
3zei.a:awh,plp
2q3d.a:pda
[1] 2q3b.a
0.8
0.9 0.8 0.7
[1] 2q3c.a 0.9
0.8
1.0 1.0
[1] 3zei.a 0.4 0.7
0.7
0.6
[2] 2q3d.a 0.1 12 8.0
0.1
[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
2q3b.a
2q3c.a
3zei.a
2q3d.a
[1] 2q3b.a
0
.02 .02 .39
[1] 2q3c.a .02
0
.02 .39
[1] 3zei.a .02 .02
0
.39
[2] 2q3d.a .39 .39 .39
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
2q3b.a
2q3c.a
3zei.a
2q3d.a
[1] 2q3b.a
0
0.7 0.3 3.0
[1] 2q3c.a 0.7
0
0.5 2.5
[1] 3zei.a 0.3 0.5
0
2.9
[2] 2q3d.a 3.0 2.5 2.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2q3b.a
2q3c.a
3zei.a
2q3d.a
[1] 2q3b.a
0
0.8 0.5 3.1
[1] 2q3c.a 0.8
0
0.7 2.6
[1] 3zei.a 0.5 0.7
0
2.9
[2] 2q3d.a 3.1 2.6 2.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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