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PYLS_METMA_185_454

Pyrrolysine--tRNA ligase [Class-II aminoacyl-tRNA synthetase family]

Composition of the binding site

Protein chains monomer
A1 (PYLS_METMA):278, 284, 287, 288, 299, 300, 330, 381:384278, 284, 287, 288, 299, 300, 330, 381:384
Cofactors (cF):anp/yly
Metals (Me):Mg

Full PDB list

2e3c, 2q7e, 2q7g, 2q7h, 2zce, 2zim, 2zin, 2zio, 3qtc, 3vqv, 3vqw, 3vqx, 3vqy, 4bw9, 4bwa, 4ch3, 4ch4, 4ch5, 4ch6, 4cs2, 4cs3, 4cs4, 4q6g, 4tqd, 4tqf, 4zib, 5k1p, 5k1x (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
I
2
7
8
L
2
8
4
Q
2
8
7
I
2
8
8
P
2
9
9
M
3
0
0
R
3
3
0
C
3
8
1
V
3
8
3
Y
3
8
4
[1]2q7h.a none . . . . . . . . . . yly
[1]3vqw.a none . . . . . * . - - - anp Mg
[1]4cs2.a none . . . . . . . . . F
[1]4cs4.a axz17 . . . . . . . . . F anp Mg
[2]4q6g.a none . . . . . . . . . . anp

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 cF Me
I
2
7
8
L
2
8
4
Q
2
8
7
I
2
8
8
P
2
9
9
M
3
0
0
R
3
3
0
C
3
8
1
M
3
8
2
V
3
8
3
Y
3
8
4
[1]2q7h.a . * . . . . . . . . . yly
[1]3vqw.a . * . . . * . - - - - anp Mg
[1]4cs2.a . . . . . * . . . . F
[1]4cs4.a . . . . . . . . . . F anp Mg
[2]4q6g.a . . . . . . . . S * . anp

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
2q7h.a is apo
3vqw.a is apo
4cs2.a is apo
4cs4.a:axz
4q6g.a is apo
[1] 2q7h.a
-
- - 2.2 -
[1] 3vqw.a -
-
- 1.9 -
[1] 4cs2.a - -
-
1.3 -
[1] 4cs4.a - - -
0.1
-
[2] 4q6g.a - - - 3.8
-
[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
2q7h.a
3vqw.a
4cs2.a
4cs4.a
4q6g.a
[1] 2q7h.a
0
.06 .25 .19 .33
[1] 3vqw.a .06
0
.25 .18 .32
[1] 4cs2.a .25 .25
0
.11 .35
[1] 4cs4.a .19 .18 .11
0
.35
[2] 4q6g.a .33 .32 .35 .35
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
2q7h.a
3vqw.a
4cs2.a
4cs4.a
4q6g.a
[1] 2q7h.a
0
0.4 0.7 0.7 1.2
[1] 3vqw.a 0.4
0
0.8 0.8 0.6
[1] 4cs2.a 0.7 0.8
0
0.7 1.2
[1] 4cs4.a 0.7 0.8 0.7
0
1.4
[2] 4q6g.a 1.2 0.6 1.2 1.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
2q7h.a
3vqw.a
4cs2.a
4cs4.a
4q6g.a
[1] 2q7h.a
0
0.7 1.0 0.9 1.4
[1] 3vqw.a 0.7
0
1.3 1.2 1.0
[1] 4cs2.a 1.0 1.3
0
0.8 1.5
[1] 4cs4.a 0.9 1.2 0.8
0
1.6
[2] 4q6g.a 1.4 1.0 1.5 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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