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EPMA_ECOLI_2_325

Elongation factor P--(R)-beta-lysine ligase [Class-II aminoacyl-tRNA synthetase family. EpmA subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EPMA_ECOLI):R: Substrate binding (76, 78)
100, 102, 107:109, 112, 114, 118, 222, 244:247, 249, 251, 296:298, 300, 303, 314
76, 78, 100, 102, 107:109, 112, 114, 118, 222, 244:247, 249, 251, 296:298, 300, 303, 314

Full PDB list

3a5y, 3a5z, 3g1z (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
S
7
6
E
7
8
R
1
0
0
E
1
0
2
Y
1
0
7
H
1
0
8
N
1
0
9
F
1
1
2
M
1
1
4
Y
1
1
8
E
2
4
4
L
2
4
5
A
2
4
6
N
2
4
7
F
2
4
9
E
2
5
1
G
2
9
6
V
2
9
7
A
2
9
8
G
3
0
0
R
3
0
3
L
3
1
4
[1]3a5y.b kaa32 . . . . . . . . . . . . . . . . . . . . . .
[1]3g1z.a amp23 . . . . H . . . . . . . . . . . . . . . . .

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
S
7
6
E
7
8
R
1
0
0
E
1
0
2
Y
1
0
7
H
1
0
8
N
1
0
9
F
1
1
2
M
1
1
4
Y
1
1
8
L
2
2
2
E
2
4
4
L
2
4
5
A
2
4
6
N
2
4
7
F
2
4
9
E
2
5
1
G
2
9
6
V
2
9
7
A
2
9
8
G
3
0
0
R
3
0
3
L
3
1
4
[1]3a5y.b . . . . . . . . . . . . . . . . . . . . . . .
[1]3g1z.a . . . . H . . . . . . . . . . . . . . . . . .

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
3a5y.b:kaa
3g1z.a:amp
[1] 3a5y.b
0
0
[1] 3g1z.a 0.9
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
3a5y.b
3g1z.a
[1] 3a5y.b
0
.04
[1] 3g1z.a .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
3a5y.b
3g1z.a
[1] 3a5y.b
0
0.6
[1] 3g1z.a 0.6
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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3a5y.b
3g1z.a
[1] 3a5y.b
0
1.1
[1] 3g1z.a 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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