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CAPP_ECOLI_1_883

Phosphoenolpyruvate carboxylase [PEPCase type 1 family]

Composition of the binding site

Protein chains monomer
A1 (CAPP_ECOLI):248, 396, 504, 506, 538, 540, 543, 580, 581, 611, 699, 713, 715248, 396, 504, 506, 538, 540, 543, 580, 581, 611, 699, 713, 715
Metals (Me):Mn

Full PDB list

1fiy, 1jqn, 1qb4 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
W
2
4
8
R
3
9
6
E
5
0
6
M
5
3
8
G
5
4
0
D
5
4
3
G
5
8
0
R
5
8
1
R
6
9
9
R
7
1
3
[1]1jqn.a dco12 . . . . . . . . . . Mn
[2]1qb4.a none . . . . . . . . . . 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

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PDB.ch
A1 Me
W
2
4
8
R
3
9
6
L
5
0
4
E
5
0
6
M
5
3
8
G
5
4
0
D
5
4
3
G
5
8
0
R
5
8
1
T
6
1
1
R
6
9
9
R
7
1
3
I
7
1
5
[1]1jqn.a . . . . . . . . . . . . . Mn
[2]1qb4.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
1jqn.a:dco
1qb4.a is apo
[1] 1jqn.a
0.3
-
[2] 1qb4.a 3.7
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
1jqn.a
1qb4.a
[1] 1jqn.a
0
.28
[2] 1qb4.a .28
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1jqn.a
1qb4.a
[1] 1jqn.a
0
0.7
[2] 1qb4.a 0.7
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
1jqn.a
1qb4.a
[1] 1jqn.a
0
1.6
[2] 1qb4.a 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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