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MENH_ECOLI_1_252

2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase [AB hydrolase superfamily. MenH family]

Composition of the binding site

Protein chains monomer
A1 (MENH_ECOLI):22, 23, 85:87, 90, 124, 147, 148, 15322, 23, 85:87, 90, 124, 147, 148, 153

Full PDB list

4gdm, 4gec, 4geg, 4mxd, 4myd, 4mys (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
G
2
2
F
2
3
Y
8
5
S
8
6
L
8
7
R
9
0
R
1
2
4
W
1
4
7
Y
1
4
8
F
1
5
3
[1]4gdm.a none . . . . . . . . . .
[1]4gec.a none . . . . . . A . . .
[1]4geg.b none . . F . . . . . . .
[1]4myd.a 16417 . . . . . . . . . .

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
G
2
2
F
2
3
Y
8
5
S
8
6
L
8
7
R
9
0
R
1
2
4
W
1
4
7
Y
1
4
8
F
1
5
3
[1]4gdm.a . . . . . . . . . .
[1]4gec.a . . . . . . A . . .
[1]4geg.b . . F . . . . . . .
[1]4myd.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
4gdm.a is apo
4gec.a is apo
4geg.b is apo
4myd.a:164
[1] 4gdm.a
-
- - 0.2
[1] 4gec.a -
-
- 0.2
[1] 4geg.b - -
-
0.2
[1] 4myd.a - - -
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
4gdm.a
4gec.a
4geg.b
4myd.a
[1] 4gdm.a
0
0 0 .02
[1] 4gec.a 0
0
0 .02
[1] 4geg.b 0 0
0
.02
[1] 4myd.a .02 .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
4gdm.a
4gec.a
4geg.b
4myd.a
[1] 4gdm.a
0
0.3 0.2 0.3
[1] 4gec.a 0.3
0
0.3 0.3
[1] 4geg.b 0.2 0.3
0
0.2
[1] 4myd.a 0.3 0.3 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
4gdm.a
4gec.a
4geg.b
4myd.a
[1] 4gdm.a
0
0.3 0.4 0.4
[1] 4gec.a 0.3
0
0.3 0.4
[1] 4geg.b 0.4 0.3
0
0.4
[1] 4myd.a 0.4 0.4 0.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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