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ATGT_PYRHO_1_582

tRNA-guanine(15) transglycosylase [Archaeosine tRNA-ribosyltransferase family]

Composition of the binding site

Protein chains monomer
A1 (ATGT_PYRHO):39, 95, 98, 99, 102, 127, 130, 132, 167, 169, 195:198, 229, 230, 249:251, 25539, 95, 98, 99, 102, 127, 130, 132, 167, 169, 195:198, 229, 230, 249:251, 255

Full PDB list

1iq8, 1it7, 1it8, 1j2b (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
D
9
5
S
9
8
F
9
9
M
1
0
2
T
1
2
7
D
1
3
0
P
1
3
2
Q
1
6
9
G
1
9
5
G
1
9
6
V
1
9
7
V
1
9
8
F
2
2
9
G
2
3
0
D
2
4
9
L
2
5
5
[1]1it7.a gun11 . . . . . . . . . . . . . . . .
[1]1it7.b none . . . . . . . . . . . . . . . .
[1]1it8.a pq013 . . . . . . . . . . . . . . . .
[1]1j2b.b G23 . . . . . . . . . . . . . . . .

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
V
3
9
D
9
5
S
9
8
F
9
9
M
1
0
2
T
1
2
7
D
1
3
0
P
1
3
2
T
1
6
7
Q
1
6
9
G
1
9
5
G
1
9
6
V
1
9
7
V
1
9
8
F
2
2
9
G
2
3
0
D
2
4
9
S
2
5
0
A
2
5
1
L
2
5
5
[1]1it7.a . . . . . . . . . . . . . . . . . . . .
[1]1it7.b . . . . . . . . . . . . . . . . . . . .
[1]1it8.a . . . . . . . . . . . . . . . . . . . .
[1]1j2b.b . . . . . . . . . . . . . . . . . . . .

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
1it7.a:gun
1it7.b is apo
1it8.a:pq0
1j2b.b:G
[1] 1it7.a
0
- 0 0.2
[1] 1it7.b 0
-
0.2 0.1
[1] 1it8.a 0 -
0
0.3
[1] 1j2b.b 0.2 - 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
1it7.a
1it7.b
1it8.a
1j2b.b
[1] 1it7.a
0
.01 0 .02
[1] 1it7.b .01
0
.02 .03
[1] 1it8.a 0 .02
0
.02
[1] 1j2b.b .02 .03 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1it7.a
1it7.b
1it8.a
1j2b.b
[1] 1it7.a
0
0.4 0.2 0.6
[1] 1it7.b 0.4
0
0.5 0.7
[1] 1it8.a 0.2 0.5
0
0.5
[1] 1j2b.b 0.6 0.7 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1it7.a
1it7.b
1it8.a
1j2b.b
[1] 1it7.a
0
0.6 0.3 0.9
[1] 1it7.b 0.6
0
0.7 1.1
[1] 1it8.a 0.3 0.7
0
0.9
[1] 1j2b.b 0.9 1.1 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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