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CYSM_MYCTU_2_323

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CYSM_MYCTU):R: Pyridoxal phosphate binding (184, 185)
51, 78:82, 109, 151, 152, 182, 183, 208:210, 215:222, 242:244, 247, 264, 265, 268, 323
51, 78:82, 109, 151, 152, 182:185, 208:210, 215:222, 242:244, 247, 264, 265, 268, 323

Full PDB list

3dki, 3dwg, 3dwi, 3fgp, 5i6d, 5i7a, 5i7h, 5i7o, 5i7r, 5iw8, 5iwc (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
5
1
T
7
8
S
7
9
G
8
0
N
8
1
T
8
2
R
1
0
9
Q
1
5
1
Y
1
5
2
G
1
8
2
L
1
8
3
G
1
8
4
T
1
8
5
A
2
0
8
E
2
0
9
P
2
1
0
A
2
1
8
L
2
1
9
R
2
2
0
N
2
2
1
M
2
2
2
V
2
4
2
A
2
4
7
I
2
6
4
S
2
6
5
A
2
6
8
A
3
2
3
[1]3dwi.b none . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]5i6d.d au620 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i7a.d 68q21 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i7h.d 68v20 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i7o.d s1620 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i7r.b 68w25 . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]5iw8.b 6ec26 . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]5iwc.a 6eq26 . . . . . . . . . . . . . . . . - - - - - . . . . . -

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
K
5
1
T
7
8
S
7
9
G
8
0
N
8
1
T
8
2
R
1
0
9
Q
1
5
1
Y
1
5
2
G
1
8
2
L
1
8
3
G
1
8
4
T
1
8
5
A
2
0
8
E
2
0
9
P
2
1
0
G
2
1
5
V
2
1
6
Y
2
1
7
A
2
1
8
L
2
1
9
R
2
2
0
N
2
2
1
M
2
2
2
V
2
4
2
G
2
4
3
A
2
4
4
A
2
4
7
I
2
6
4
S
2
6
5
A
2
6
8
A
3
2
3
[1]3dwi.b . . . . . . . . . . . . . . . . . * . * * . . . . . . . . . . -
[1]5i6d.d . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . .
[1]5i7a.d . . . . . . . . . . . . . . . . - - - . * . . . . . . . . . . .
[1]5i7h.d . . . . . . . . . . . . . . . . - - . . * . . . . . . . . . . .
[1]5i7o.d . . . . . . . . . . . . . . . . - - . . * . . . . . . . . . . .
[1]5i7r.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]5iw8.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]5iwc.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
3dwi.b is apo
5i6d.d:au6
5i7a.d:68q
5i7h.d:68v
5i7o.d:s16
5i7r.b:68w
5iw8.b:6ec
5iwc.a:6eq
[1] 3dwi.b
-
6.0 6.7 5.5 5.6 7.4 7.6 8.4
[1] 5i6d.d -
0
0.1 0.1 0 1.8 1.9 1.8
[1] 5i7a.d - 0
0
0 0 1.5 1.6 1.9
[1] 5i7h.d - 0.1 0.3
0.1
0.1 1.9 1.9 1.9
[1] 5i7o.d - 0.1 0.3 0.1
0.1
1.8 2.0 2.0
[1] 5i7r.b - 0 0.1 0.1 0.1
0
0 0
[1] 5iw8.b - 0.4 0.5 0.6 0.3 0
0
0.2
[1] 5iwc.a - 0.1 0.1 0.1 0.1 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
3dwi.b
5i6d.d
5i7a.d
5i7h.d
5i7o.d
5i7r.b
5iw8.b
5iwc.a
[1] 3dwi.b
0
.21 .23 .21 .22 .26 .26 .26
[1] 5i6d.d .21
0
.02 .01 0 .06 .06 .06
[1] 5i7a.d .23 .02
0
.02 .02 .06 .06 .06
[1] 5i7h.d .21 .01 .02
0
0 .06 .06 .06
[1] 5i7o.d .22 0 .02 0
0
.07 .07 .07
[1] 5i7r.b .26 .06 .06 .06 .07
0
.02 0
[1] 5iw8.b .26 .06 .06 .06 .07 .02
0
.02
[1] 5iwc.a .26 .06 .06 .06 .07 0 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.2 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
3dwi.b
5i6d.d
5i7a.d
5i7h.d
5i7o.d
5i7r.b
5iw8.b
5iwc.a
[1] 3dwi.b
0
4.9 3.8 4.3 4.3 3.6 3.7 0.7
[1] 5i6d.d 4.9
0
0.8 0.3 0.2 3.1 3.5 1.3
[1] 5i7a.d 3.8 0.8
0
0.8 0.8 2.5 2.9 1.8
[1] 5i7h.d 4.3 0.3 0.8
0
0.3 2.5 3.1 1.3
[1] 5i7o.d 4.3 0.2 0.8 0.3
0
2.5 3.1 1.3
[1] 5i7r.b 3.6 3.1 2.5 2.5 2.5
0
1.7 0.8
[1] 5iw8.b 3.7 3.5 2.9 3.1 3.1 1.7
0
1.1
[1] 5iwc.a 0.7 1.3 1.8 1.3 1.3 0.8 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.5 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
3dwi.b
5i6d.d
5i7a.d
5i7h.d
5i7o.d
5i7r.b
5iw8.b
5iwc.a
[1] 3dwi.b
0
5.4 4.0 5.0 5.0 4.4 4.4 1.1
[1] 5i6d.d 5.4
0
1.2 0.5 0.6 3.6 4.1 1.8
[1] 5i7a.d 4.0 1.2
0
1.2 1.3 3.4 3.3 2.5
[1] 5i7h.d 5.0 0.5 1.2
0
0.6 3.2 3.8 1.8
[1] 5i7o.d 5.0 0.6 1.3 0.6
0
3.2 3.7 1.7
[1] 5i7r.b 4.4 3.6 3.4 3.2 3.2
0
2.5 1.1
[1] 5iw8.b 4.4 4.1 3.3 3.8 3.7 2.5
0
1.9
[1] 5iwc.a 1.1 1.8 2.5 1.8 1.7 1.1 1.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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