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DT3E_PSECI_1_290

D-tagatose 3-epimerase [Hyi family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DT3E_PSECI):R: Substrate binding (185, 188)
7, 15, 35, 37, 66:68, 107, 108, 113, 152, 154, 158, 211, 217, 246, 248, 259
7, 15, 35, 37, 66:68, 107, 108, 113, 152, 154, 158, 185, 188, 211, 217, 246, 248, 259
Metals (Me):Mn

Full PDB list

2ou4, 2qul, 2qum, 2qun, 4pfh, 4pgl, 4q7i, 4xsl, 4xsm, 4ytq, 4ytr, 4yts, 4ytt, 4ytu, 5j8l (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
F
7
W
1
5
S
3
7
C
6
6
I
6
7
G
6
8
G
1
0
7
L
1
0
8
W
1
1
3
E
1
5
2
V
1
5
4
E
1
5
8
D
1
8
5
H
1
8
8
H
2
1
1
R
2
1
7
E
2
4
6
F
2
4
8
V
2
5
9
[1]2qul.a none . . . . . . . . . . . . . . . . . . . Mn
[1]2qum.a tag12 . . . . . . . . . . . . . . . . . . . Mn
[1]2qun.a fud12 . . . . . . . . . . . . . . . . . . . Mn
[1]4pfh.b fud,psj24 . . N . . . . . . . . . . . . . . . . Mn
[1]4pgl.a ltg,sol24 . . . . . . . . . . . . . . . . . . . Mn
[1]4xsl.a none . . . S . . . . . . . . . . . . . . . Mn
[1]4xsm.a tlz12 . . . S . . . . . . . . . . . . . . . Mn
[1]4ytq.a tgd11 . . . S . . . . . . . . . . . . . . . Mn
[1]4yts.c tgs11 . . . S . . . . . . . . . . . . . . . Mn
[1]4ytt.a pud11 . . . S . . . . . . . . . . . . . . . Mn
[1]4ytu.a ler8 . . . S . . . . . . . . . . . . . . . Mn
[1]5j8l.a tgj11 . . . S . . . . . . . . . . . . . . . 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
F
7
W
1
5
E
3
5
S
3
7
C
6
6
I
6
7
G
6
8
G
1
0
7
L
1
0
8
W
1
1
3
E
1
5
2
V
1
5
4
E
1
5
8
D
1
8
5
H
1
8
8
H
2
1
1
R
2
1
7
E
2
4
6
F
2
4
8
V
2
5
9
[1]2qul.a . . . . . . . . . . . . . . . . . . . . Mn
[1]2qum.a . . . . . . . . . . . . . . . . . . . . Mn
[1]2qun.a . . . . . . . . . . . . . . . . . . . . Mn
[1]4pfh.b . . . N . . . . . . . . . . . . . . . . Mn
[1]4pgl.a . . . . . . . . . . . . . . . . . . . . Mn
[1]4xsl.a . . . . S . . . . . . . . . . . . . . . Mn
[1]4xsm.a . . . . S . . . . . . . . . . . . . . . Mn
[1]4ytq.a . . . . S . . . . . . . . . . . . . . . Mn
[1]4yts.c . . . . S . . . . . . . . . . . . . . . Mn
[1]4ytt.a . . . . S . . . . . . . . . . . . . . . Mn
[1]4ytu.a . . . . S . . . . . . . . . . . . . . . Mn
[1]5j8l.a . . . . S . . . . . . . . . . . . . . . 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
2qul.a is apo
2qum.a:tag
2qun.a:fud
4pfh.b:fud,psj
4pgl.a:ltg,sol
4xsl.a is apo
4xsm.a:tlz
4ytq.a:tgd
4yts.c:tgs
4ytt.a:pud
4ytu.a:ler
5j8l.a:tgj
[1] 2qul.a
-
0.3 0.2 0.4 0.2 - 0.7 0.3 0.2 0.2 0.1 0.2
[1] 2qum.a -
0.1
0.2 0.4 0.1 - 0.7 0.3 0.2 0 0.1 0
[1] 2qun.a - 0.1
0.2
0.4 0.2 - 0.6 0.1 0.2 0.1 0.1 0.1
[1] 4pfh.b - 0.3 0.3
0.4
0.2 - 0.7 0.1 0.2 0.1 0.1 0.2
[1] 4pgl.a - 0.3 0.1 0.4
0.1
- 0.8 0.1 0.3 0.1 0.1 0.1
[1] 4xsl.a - 0.2 0.3 0.3 0.2
-
0.5 0.3 0.2 0.1 0.1 0.2
[1] 4xsm.a - 0.2 0.2 0.3 0.2 -
0.2
0.3 0.2 0.1 0 0.1
[1] 4ytq.a - 0.2 0.2 0.3 0.2 - 0.5
0.2
0.2 0.1 0.1 0.2
[1] 4yts.c - 0.2 0.2 0.3 0.2 - 0.5 0
0.1
0.1 0.2 0.1
[1] 4ytt.a - 0.1 0.1 0.3 0.2 - 0.6 0.2 0.2
0.1
0.1 0
[1] 4ytu.a - 0.2 0.1 0.2 0.1 - 0.3 0.1 0.2 0.1
0
0.1
[1] 5j8l.a - 0.1 0.1 0.3 0.2 - 0.3 0.1 0.2 0.1 0.1
0.1
[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
2qul.a
2qum.a
2qun.a
4pfh.b
4pgl.a
4xsl.a
4xsm.a
4ytq.a
4yts.c
4ytt.a
4ytu.a
5j8l.a
[1] 2qul.a
0
.03 .01 .03 .02 .02 .04 .01 .03 .01 .03 .03
[1] 2qum.a .03
0
.03 .03 .03 .03 .05 .04 .04 .04 .05 .05
[1] 2qun.a .01 .03
0
.02 .02 .02 .04 .01 .02 .01 .02 .03
[1] 4pfh.b .03 .03 .02
0
.02 .04 .06 .03 .04 .03 .04 .05
[1] 4pgl.a .02 .03 .02 .02
0
.03 .05 .02 .04 .02 .04 .04
[1] 4xsl.a .02 .03 .02 .04 .03
0
.02 .01 .03 .01 .03 .02
[1] 4xsm.a .04 .05 .04 .06 .05 .02
0
.03 .04 .03 .02 .02
[1] 4ytq.a .01 .04 .01 .03 .02 .01 .03
0
.02 0 .02 .02
[1] 4yts.c .03 .04 .02 .04 .04 .03 .04 .02
0
.02 .03 .03
[1] 4ytt.a .01 .04 .01 .03 .02 .01 .03 0 .02
0
.02 .02
[1] 4ytu.a .03 .05 .02 .04 .04 .03 .02 .02 .03 .02
0
.02
[1] 5j8l.a .03 .05 .03 .05 .04 .02 .02 .02 .03 .02 .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
2qul.a
2qum.a
2qun.a
4pfh.b
4pgl.a
4xsl.a
4xsm.a
4ytq.a
4yts.c
4ytt.a
4ytu.a
5j8l.a
[1] 2qul.a
0
0.2 0.1 0.2 0.3 0.1 0.2 0.1 0.2 0.2 0.2 0.2
[1] 2qum.a 0.2
0
0.2 0.3 0.3 0.2 0.2 0.2 0.2 0.2 0.2 0.2
[1] 2qun.a 0.1 0.2
0
0.3 0.3 0.1 0.2 0.2 0.2 0.1 0.2 0.2
[1] 4pfh.b 0.2 0.3 0.3
0
0.2 0.2 0.3 0.2 0.3 0.2 0.3 0.2
[1] 4pgl.a 0.3 0.3 0.3 0.2
0
0.3 0.3 0.3 0.3 0.3 0.3 0.3
[1] 4xsl.a 0.1 0.2 0.1 0.2 0.3
0
0.2 0.2 0.2 0.2 0.2 0.2
[1] 4xsm.a 0.2 0.2 0.2 0.3 0.3 0.2
0
0.2 0.2 0.2 0.2 0.2
[1] 4ytq.a 0.1 0.2 0.2 0.2 0.3 0.2 0.2
0
0.2 0.1 0.2 0.1
[1] 4yts.c 0.2 0.2 0.2 0.3 0.3 0.2 0.2 0.2
0
0.1 0.2 0.2
[1] 4ytt.a 0.2 0.2 0.1 0.2 0.3 0.2 0.2 0.1 0.1
0
0.2 0.1
[1] 4ytu.a 0.2 0.2 0.2 0.3 0.3 0.2 0.2 0.2 0.2 0.2
0
0.2
[1] 5j8l.a 0.2 0.2 0.2 0.2 0.3 0.2 0.2 0.1 0.2 0.1 0.2
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
2qul.a
2qum.a
2qun.a
4pfh.b
4pgl.a
4xsl.a
4xsm.a
4ytq.a
4yts.c
4ytt.a
4ytu.a
5j8l.a
[1] 2qul.a
0
0.2 0.1 0.3 0.4 0.2 0.4 0.3 0.3 0.3 0.3 0.3
[1] 2qum.a 0.2
0
0.2 0.4 0.5 0.3 0.4 0.3 0.4 0.3 0.3 0.3
[1] 2qun.a 0.1 0.2
0
0.3 0.4 0.2 0.3 0.3 0.3 0.3 0.3 0.3
[1] 4pfh.b 0.3 0.4 0.3
0
0.4 0.3 0.4 0.3 0.4 0.3 0.4 0.3
[1] 4pgl.a 0.4 0.5 0.4 0.4
0
0.3 0.5 0.4 0.4 0.4 0.4 0.4
[1] 4xsl.a 0.2 0.3 0.2 0.3 0.3
0
0.3 0.2 0.3 0.2 0.2 0.2
[1] 4xsm.a 0.4 0.4 0.3 0.4 0.5 0.3
0
0.3 0.3 0.3 0.3 0.3
[1] 4ytq.a 0.3 0.3 0.3 0.3 0.4 0.2 0.3
0
0.2 0.1 0.2 0.2
[1] 4yts.c 0.3 0.4 0.3 0.4 0.4 0.3 0.3 0.2
0
0.2 0.3 0.2
[1] 4ytt.a 0.3 0.3 0.3 0.3 0.4 0.2 0.3 0.1 0.2
0
0.2 0.1
[1] 4ytu.a 0.3 0.3 0.3 0.4 0.4 0.2 0.3 0.2 0.3 0.2
0
0.2
[1] 5j8l.a 0.3 0.3 0.3 0.3 0.4 0.2 0.3 0.2 0.2 0.1 0.2
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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