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CYSK1_ARATH_2_322

Cysteine synthase 1 [Cysteine synthase/cystathionine beta- synthase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CYSK1_ARATH):R: SUTR1;2 binding (147, 148, 179:185, 219:221, 224:228, 230, 269)
R: Pyridoxal phosphate binding (181:185)
R: SAT1 binding (219:221)
45, 46, 74:78, 101, 124:126, 129, 296, 297, 302
45, 46, 74:78, 101, 124:126, 129, 147, 148, 179:185, 219:221, 224:228, 230, 269, 296, 297, 302

Full PDB list

1z7w, 1z7y, 2isq

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
4
6
T
7
4
S
7
5
G
7
6
N
7
7
T
7
8
M
1
0
1
G
1
2
4
M
1
2
5
K
1
2
6
I
1
2
9
Q
1
4
7
F
1
4
8
G
1
7
9
I
1
8
0
G
1
8
1
T
1
8
2
G
1
8
3
T
1
8
5
G
2
1
9
P
2
2
0
H
2
2
1
Q
2
2
4
G
2
2
5
I
2
2
6
G
2
2
7
A
2
2
8
F
2
3
0
S
2
6
9
P
2
9
6
S
2
9
7
Y
3
0
2
[1]1z7w.a plp15 * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1z7y.a aa524 A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2isq.a plp,TEWSDYVI87 * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
5
K
4
6
T
7
4
S
7
5
G
7
6
N
7
7
T
7
8
M
1
0
1
G
1
2
4
M
1
2
5
K
1
2
6
I
1
2
9
Q
1
4
7
F
1
4
8
G
1
7
9
I
1
8
0
G
1
8
1
T
1
8
2
G
1
8
3
G
1
8
4
T
1
8
5
G
2
1
9
P
2
2
0
H
2
2
1
Q
2
2
4
G
2
2
5
I
2
2
6
G
2
2
7
A
2
2
8
F
2
3
0
S
2
6
9
P
2
9
6
S
2
9
7
Y
3
0
2
[1]1z7w.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1z7y.a . A . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]2isq.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
1z7w.a:plp
1z7y.a:aa5
2isq.a:TEWSDYVI,plp
[1] 1z7w.a
0.6
1.4 0.8
[1] 1z7y.a 0
0.2
1.2
[1] 2isq.a 0.6 1.6
0.7
[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
1z7w.a
1z7y.a
2isq.a
[1] 1z7w.a
0
.06 .02
[1] 1z7y.a .06
0
.07
[1] 2isq.a .02 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1z7w.a
1z7y.a
2isq.a
[1] 1z7w.a
0
0.4 0.4
[1] 1z7y.a 0.4
0
0.5
[1] 2isq.a 0.4 0.5
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

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
1z7w.a
1z7y.a
2isq.a
[1] 1z7w.a
0
0.7 0.5
[1] 1z7y.a 0.7
0
0.8
[1] 2isq.a 0.5 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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