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3MG2_ECOLI_1_282

DNA-3-methyladenine glycosylase 2 [Alkylbase DNA glycosidase AlkA family]

Composition of the binding site

Protein chains monomer
A1 (3MG2_ECOLI):123:128, 178, 218, 219, 237:239, 242123:128, 178, 218, 219, 237:239, 242

Full PDB list

1diz, 1mpg, 1pvs, 3cvs, 3cvt, 3cw7, 3cwa, 3cws, 3cwt, 3cwu, 3d4v, 3ogd, 3oh6, 3oh9 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
G
1
2
3
Q
1
2
4
L
1
2
5
V
1
2
6
S
1
2
7
V
1
2
8
W
2
1
8
D
2
3
7
D
2
3
8
Y
2
3
9
[1]1diz.b nriT31 . . . . . . . . . .
[1]1mpg.b none . . . . . . . . . .
[1]1pvs.a 7hp10 . . . . . . . . . .
[1]3cvs.a G19 . . . . . . . . . .
[1]3cwa.a 8og20 . . . . . . . . . .
[1]3ogd.a T20 . . C . . . . . . .
[1]3oh6.a A21 . . . . . . . . . C
[1]3oh9.a C19 . . . . . . . . . C

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
G
1
2
3
Q
1
2
4
L
1
2
5
V
1
2
6
S
1
2
7
V
1
2
8
R
1
7
8
W
2
1
8
T
2
1
9
D
2
3
7
D
2
3
8
Y
2
3
9
K
2
4
2
[1]1diz.b . . . . . . . . . . . . .
[1]1mpg.b . . * . . . . . . . . . .
[1]1pvs.a . . * . . . . . . . . * .
[1]3cvs.a . . . . . . . . . . . . .
[1]3cwa.a . . . . . . . . . . . . .
[1]3ogd.a . . C . . . . . . . . * .
[1]3oh6.a . . . . . . . . . . . C .
[1]3oh9.a . . . . . . . . . . . C .

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
1diz.b:nriT
1mpg.b is apo
1pvs.a:7hp
3cvs.a:G
3cwa.a:8og
3ogd.a:T
3oh6.a:A
3oh9.a:C
[1] 1diz.b
0
- 0.1 0 0 0 0 0
[1] 1mpg.b 1.6
-
0.3 1.4 1.2 1.0 1.0 0.7
[1] 1pvs.a 2.6 -
0
1.0 1.2 1.6 2.2 1.3
[1] 3cvs.a 0 - 0
0
0 0 0 0
[1] 3cwa.a 0.1 - 0 0
0
0 0 0
[1] 3ogd.a 1.3 - 0.1 0 0
0
0 0
[1] 3oh6.a 0.1 - 0 0 0 0
0
0
[1] 3oh9.a 0.3 - 0.1 0.1 0.1 0.1 0.1
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
1diz.b
1mpg.b
1pvs.a
3cvs.a
3cwa.a
3ogd.a
3oh6.a
3oh9.a
[1] 1diz.b
0
.15 .19 .01 .01 .09 0 .03
[1] 1mpg.b .15
0
.19 .14 .14 .24 .15 .16
[1] 1pvs.a .19 .19
0
.20 .19 .11 .19 .18
[1] 3cvs.a .01 .14 .20
0
.01 .09 .01 .04
[1] 3cwa.a .01 .14 .19 .01
0
.10 .01 .03
[1] 3ogd.a .09 .24 .11 .09 .10
0
.09 .09
[1] 3oh6.a 0 .15 .19 .01 .01 .09
0
.03
[1] 3oh9.a .03 .16 .18 .04 .03 .09 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
1diz.b
1mpg.b
1pvs.a
3cvs.a
3cwa.a
3ogd.a
3oh6.a
3oh9.a
[1] 1diz.b
0
0.7 0.7 0.5 0.4 2.5 2.4 2.1
[1] 1mpg.b 0.7
0
0.5 0.7 0.7 2.6 2.5 2.2
[1] 1pvs.a 0.7 0.5
0
0.5 0.5 2.4 2.4 2.1
[1] 3cvs.a 0.5 0.7 0.5
0
0.1 2.3 2.3 2.0
[1] 3cwa.a 0.4 0.7 0.5 0.1
0
2.3 2.3 2.0
[1] 3ogd.a 2.5 2.6 2.4 2.3 2.3
0
0.6 0.8
[1] 3oh6.a 2.4 2.5 2.4 2.3 2.3 0.6
0
0.4
[1] 3oh9.a 2.1 2.2 2.1 2.0 2.0 0.8 0.4
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

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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
1diz.b
1mpg.b
1pvs.a
3cvs.a
3cwa.a
3ogd.a
3oh6.a
3oh9.a
[1] 1diz.b
0
1.3 1.7 0.7 0.8 2.6 2.5 2.3
[1] 1mpg.b 1.3
0
1.6 1.3 1.3 2.8 2.7 2.5
[1] 1pvs.a 1.7 1.6
0
1.6 1.6 2.7 2.4 2.2
[1] 3cvs.a 0.7 1.3 1.6
0
0.2 2.5 2.2 2.0
[1] 3cwa.a 0.8 1.3 1.6 0.2
0
2.5 2.2 2.0
[1] 3ogd.a 2.6 2.8 2.7 2.5 2.5
0
1.2 1.2
[1] 3oh6.a 2.5 2.7 2.4 2.2 2.2 1.2
0
0.7
[1] 3oh9.a 2.3 2.5 2.2 2.0 2.0 1.2 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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