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DHBE_BACSU_1_539

2,3-dihydroxybenzoate-AMP ligase [ATP-dependent AMP-binding enzyme family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DHBE_BACSU):R: Substrate binding (234, 235)
190:192, 236, 240, 307:309, 329:333, 337, 353, 413, 425, 428, 519
190:192, 234:236, 240, 307:309, 329:333, 337, 353, 413, 425, 428, 519

Full PDB list

1md9, 1mdb, 1mdf

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
1
9
1
G
1
9
2
H
2
3
4
N
2
3
5
Y
2
3
6
S
2
4
0
G
3
0
7
A
3
0
8
K
3
0
9
V
3
2
9
F
3
3
0
G
3
3
1
M
3
3
2
A
3
3
3
V
3
3
7
Q
3
5
3
D
4
1
3
V
4
2
5
R
4
2
8
K
5
1
9
[1]1md9.a amp,dbh34 . . . . . . . . . . . . * . . . . . . .
[1]1mdb.a amp.dbh33 . . . . . . . . . . . . . . . . . . . .
[1]1mdf.a none . . . . . . . . . . . . . . . . . . . .

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
S
1
9
0
G
1
9
1
G
1
9
2
H
2
3
4
N
2
3
5
Y
2
3
6
S
2
4
0
G
3
0
7
A
3
0
8
K
3
0
9
V
3
2
9
F
3
3
0
G
3
3
1
M
3
3
2
A
3
3
3
V
3
3
7
Q
3
5
3
D
4
1
3
V
4
2
5
R
4
2
8
K
5
1
9
[1]1md9.a . . . . . . . . . . . . . * . . . . . . .
[1]1mdb.a . . . . . . . . . . . . . . . . . . . . .
[1]1mdf.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
1md9.a:amp,dbh
1mdb.a:amp.dbh
1mdf.a is apo
[1] 1md9.a
0.7
0.2 -
[1] 1mdb.a 1.2
0.4
-
[1] 1mdf.a 2.6 0.9
-
[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
1md9.a
1mdb.a
1mdf.a
[1] 1md9.a
0
.03 .10
[1] 1mdb.a .03
0
.07
[1] 1mdf.a .10 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1md9.a
1mdb.a
1mdf.a
[1] 1md9.a
0
0.9 0.9
[1] 1mdb.a 0.9
0
0.3
[1] 1mdf.a 0.9 0.3
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
1md9.a
1mdb.a
1mdf.a
[1] 1md9.a
0
0.9 1.0
[1] 1mdb.a 0.9
0
0.4
[1] 1mdf.a 1.0 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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