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DPES_CLOCE_1_293

D-psicose 3-epimerase [Hyi family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DPES_CLOCE):R: Substrate binding (183, 186)
6, 14, 65:67, 106, 112, 150, 152, 156, 209, 215, 244, 246, 257
6, 14, 65:67, 106, 112, 150, 152, 156, 183, 186, 209, 215, 244, 246, 257
Metals (Me):Mn

Full PDB list

3vni, 3vnj, 3vnk, 3vnl, 3vnm

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Y
6
W
1
4
H
6
6
G
6
7
G
1
0
6
W
1
1
2
E
1
5
0
L
1
5
2
E
1
5
6
D
1
8
3
H
1
8
6
H
2
0
9
R
2
1
5
E
2
4
4
F
2
4
6
[1]3vni.b none . . . . . . . . . . . . . . . Mn
[1]3vnj.b psj12 . . . . . . . . . . . . . . . Mn
[1]3vnk.b fud12 . . . . . . . . . . . . . . . Mn
[1]3vnl.a tag12 . . . . . . . . . . . . . . . Mn
[1]3vnm.a sdd12 . . . . . . . . . . . . . . . Mn

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 Me
Y
6
W
1
4
G
6
5
H
6
6
G
6
7
G
1
0
6
W
1
1
2
E
1
5
0
L
1
5
2
E
1
5
6
D
1
8
3
H
1
8
6
H
2
0
9
R
2
1
5
E
2
4
4
F
2
4
6
I
2
5
7
[1]3vni.b . . . . . . . . . . . . . . . . . Mn
[1]3vnj.b . . . . . . . . . . . . . . . . . Mn
[1]3vnk.b . . . . . . . . . . . . . . . . . Mn
[1]3vnl.a . . . . . . . . . . . . . . . . . Mn
[1]3vnm.a . . . . . . . . . . . . . . . . . Mn

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
3vni.b is apo
3vnj.b:psj
3vnk.b:fud
3vnl.a:tag
3vnm.a:sdd
[1] 3vni.b
-
0.1 0.1 0.2 0.1
[1] 3vnj.b -
0
0.2 0.2 0.2
[1] 3vnk.b - 0.1
0.1
0.3 0.2
[1] 3vnl.a - 0.3 0.2
0.2
0.1
[1] 3vnm.a - 0.3 0.3 0.3
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
3vni.b
3vnj.b
3vnk.b
3vnl.a
3vnm.a
[1] 3vni.b
0
.01 .01 .01 .02
[1] 3vnj.b .01
0
.01 .01 .02
[1] 3vnk.b .01 .01
0
.01 .03
[1] 3vnl.a .01 .01 .01
0
.02
[1] 3vnm.a .02 .02 .03 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
3vni.b
3vnj.b
3vnk.b
3vnl.a
3vnm.a
[1] 3vni.b
0
0.3 0.3 0.3 0.3
[1] 3vnj.b 0.3
0
0.1 0.1 0.2
[1] 3vnk.b 0.3 0.1
0
0.1 0.2
[1] 3vnl.a 0.3 0.1 0.1
0
0.1
[1] 3vnm.a 0.3 0.2 0.2 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
3vni.b
3vnj.b
3vnk.b
3vnl.a
3vnm.a
[1] 3vni.b
0
0.3 0.4 0.3 0.4
[1] 3vnj.b 0.3
0
0.1 0.2 0.3
[1] 3vnk.b 0.4 0.1
0
0.2 0.4
[1] 3vnl.a 0.3 0.2 0.2
0
0.3
[1] 3vnm.a 0.4 0.3 0.4 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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