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MTH1_HAEPH_1_327

Modification methylase HhaI [Class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (MTH1_HAEPH):D: SAM-dependent MTase C5-type (18:24, 39:42, 60:62, 78:81, 85, 86, 96, 97, 99, 100, 119:122, 163, 165, 250, 252, 253, 285, 303:306)18:24, 39:42, 60:62, 78:81, 85, 86, 96, 97, 99, 100, 119:122, 163, 165, 250, 252, 253, 285, 303:306

Full PDB list

10mh, 1fjx, 1hmy, 1m0e, 1mht, 1skm, 1svu, 2c7o, 2c7p, 2c7q, 2c7r, 2hmy, 2hr1, 2i9k, 2uyc, 2uyh, 2uz4, 2z6a, 2z6q, 2z6u, 2zcj, 3eeo, 3mht, 4mht, 5ciy, 5lod, 5mht, 6mht, 7mht, 8mht, 9mht (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
8
A
1
9
G
2
0
L
2
1
G
2
3
F
2
4
N
3
9
E
4
0
W
4
1
D
4
2
D
6
0
I
6
1
G
7
8
F
7
9
P
8
0
C
8
1
S
8
5
L
1
0
0
E
1
1
9
V
1
2
1
R
1
6
3
R
1
6
5
S
2
5
2
A
2
5
3
G
3
0
3
N
3
0
4
S
3
0
5
V
3
0
6
[1]1fjx.a sah26 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2i9k.a sah26 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2uyc.a sah26 . . . . . . . . . . . . . . . . . . . . N . . . . . . .
[1]2uz4.a sah26 . . . . . . . . . . . . . . . . . . . . . N . . . . . .
[1]2z6a.a sah26 . . . . . . . . . . . . . . . A . . . . . . . . . . . .
[1]2z6q.a sah26 . . . . . . . . . . . . . . . . . . . . . A . . . . . .
[1]2z6u.a sah26 . . . . . . . . . . . . . . . . . . A . . . . . . . . .
[1]2zcj.a sah26 . . . . . . . . . . . . . . . . . . Q . . . . . . . . .
[1]3eeo.a sam27 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4mht.a 5cm,sah46 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lod.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6mht.a 4sc,sam47 . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
F
1
8
A
1
9
G
2
0
L
2
1
G
2
2
G
2
3
F
2
4
N
3
9
E
4
0
W
4
1
D
4
2
D
6
0
I
6
1
T
6
2
G
7
8
F
7
9
P
8
0
C
8
1
S
8
5
I
8
6
S
9
6
R
9
7
T
9
9
L
1
0
0
E
1
1
9
N
1
2
0
V
1
2
1
K
1
2
2
R
1
6
3
R
1
6
5
T
2
5
0
S
2
5
2
A
2
5
3
Y
2
8
5
G
3
0
3
N
3
0
4
S
3
0
5
V
3
0
6
[1]1fjx.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G . . . . . . .
[1]2i9k.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2uyc.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . N . . . . . . . . .
[1]2uz4.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . N . . . . . . . .
[1]2z6a.a . . . . . . . . . . . . . . . . . A . . . . . . . . . . . . . . . . . . . .
[1]2z6q.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A . . . . . . . .
[1]2z6u.a . . . . . . . . . . . . . . . . . . . . . . . . A . . . . . . . . . . . . .
[1]2zcj.a . . . . . . . . . . . . . . . . . . . . . . . . Q . . . . . . . . . . . . .
[1]3eeo.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4mht.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5lod.b . . . . . . . . . . . . . . . . . . . - . . . . . . . . . * . . . . . . . .
[1]6mht.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
1fjx.a:sah
2i9k.a:sah
2uyc.a:sah
2uz4.a:sah
2z6a.a:sah
2z6q.a:sah
2z6u.a:sah
2zcj.a:sah
3eeo.a:sam
4mht.a:5cm,sah
5lod.b is apo
6mht.a:4sc,sam
[1] 1fjx.a
0.1
0.1 0 0 0 0 0.1 0.1 0.1 0.3 - 0.5
[1] 2i9k.a 0.1
0
0 0.1 0 0 0 0 0.4 0.7 - 0.9
[1] 2uyc.a 0 0
0
0 0 0 0 0 0 0.4 - 0.7
[1] 2uz4.a 0 0 0
0
0 0 0 0 0.1 0.6 - 0.5
[1] 2z6a.a 0.1 0.1 0.2 0.2
0
0 0 0.1 0.1 0.3 - 0.7
[1] 2z6q.a 0 0 0 0.1 0
0
0 0 0.1 0.3 - 0.5
[1] 2z6u.a 0.1 0 0 0.2 0 0
0
0 0.1 0.4 - 0.9
[1] 2zcj.a 0.1 0 0 0 0 0 0
0
0.1 0.4 - 0.7
[1] 3eeo.a 0.1 0 0 0 0 0 0 0
0.1
0.7 - 0.9
[1] 4mht.a 0.1 0.1 0.1 0.2 0 0 0 0 0.2
0.4
- 0.2
[1] 5lod.b 0.7 0.7 0.5 0.5 0.7 0.6 0.7 0.6 0.8 2.7
-
2.4
[1] 6mht.a 0.1 0.1 0.1 0.2 0 0 0 0.1 0 0.2 -
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
1fjx.a
2i9k.a
2uyc.a
2uz4.a
2z6a.a
2z6q.a
2z6u.a
2zcj.a
3eeo.a
4mht.a
5lod.b
6mht.a
[1] 1fjx.a
0
.02 .02 .02 .03 .02 .02 .02 .02 .02 .08 .02
[1] 2i9k.a .02
0
.02 .03 .02 .03 .01 .02 .02 .03 .07 .04
[1] 2uyc.a .02 .02
0
.01 .03 .02 .02 .02 .02 .02 .09 .02
[1] 2uz4.a .02 .03 .01
0
.04 .02 .02 .03 .02 .02 .09 .02
[1] 2z6a.a .03 .02 .03 .04
0
.03 .02 .01 .03 .02 .07 .02
[1] 2z6q.a .02 .03 .02 .02 .03
0
.03 .03 .03 .02 .09 .02
[1] 2z6u.a .02 .01 .02 .02 .02 .03
0
.01 .01 .03 .08 .03
[1] 2zcj.a .02 .02 .02 .03 .01 .03 .01
0
.02 .02 .07 .02
[1] 3eeo.a .02 .02 .02 .02 .03 .03 .01 .02
0
.03 .07 .03
[1] 4mht.a .02 .03 .02 .02 .02 .02 .03 .02 .03
0
.07 .01
[1] 5lod.b .08 .07 .09 .09 .07 .09 .08 .07 .07 .07
0
.07
[1] 6mht.a .02 .04 .02 .02 .02 .02 .03 .02 .03 .01 .07
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
1fjx.a
2i9k.a
2uyc.a
2uz4.a
2z6a.a
2z6q.a
2z6u.a
2zcj.a
3eeo.a
4mht.a
5lod.b
6mht.a
[1] 1fjx.a
0
0.3 0.3 0.3 0.3 0.5 0.3 0.3 0.3 0.3 3.7 0.6
[1] 2i9k.a 0.3
0
0.3 0.2 0.2 0.5 0.2 0.2 0.3 0.3 3.8 0.7
[1] 2uyc.a 0.3 0.3
0
0.2 0.3 0.4 0.2 0.3 0.3 0.3 3.8 0.6
[1] 2uz4.a 0.3 0.2 0.2
0
0.3 0.4 0.2 0.2 0.3 0.3 3.8 0.6
[1] 2z6a.a 0.3 0.2 0.3 0.3
0
0.5 0.2 0.2 0.3 0.3 3.8 0.6
[1] 2z6q.a 0.5 0.5 0.4 0.4 0.5
0
0.4 0.5 0.5 0.5 3.9 0.7
[1] 2z6u.a 0.3 0.2 0.2 0.2 0.2 0.4
0
0.2 0.3 0.3 3.8 0.6
[1] 2zcj.a 0.3 0.2 0.3 0.2 0.2 0.5 0.2
0
0.3 0.3 3.8 0.6
[1] 3eeo.a 0.3 0.3 0.3 0.3 0.3 0.5 0.3 0.3
0
0.4 3.8 0.6
[1] 4mht.a 0.3 0.3 0.3 0.3 0.3 0.5 0.3 0.3 0.4
0
3.8 0.5
[1] 5lod.b 3.7 3.8 3.8 3.8 3.8 3.9 3.8 3.8 3.8 3.8
0
3.7
[1] 6mht.a 0.6 0.7 0.6 0.6 0.6 0.7 0.6 0.6 0.6 0.5 3.7
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

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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
1fjx.a
2i9k.a
2uyc.a
2uz4.a
2z6a.a
2z6q.a
2z6u.a
2zcj.a
3eeo.a
4mht.a
5lod.b
6mht.a
[1] 1fjx.a
0
0.6 0.6 0.7 0.7 0.7 0.6 0.6 0.7 0.6 4.7 0.9
[1] 2i9k.a 0.6
0
0.5 0.5 0.4 0.5 0.2 0.3 0.6 0.4 4.7 0.9
[1] 2uyc.a 0.6 0.5
0
0.3 0.5 0.6 0.4 0.5 0.6 0.6 4.8 0.8
[1] 2uz4.a 0.7 0.5 0.3
0
0.5 0.6 0.5 0.5 0.6 0.6 4.7 0.8
[1] 2z6a.a 0.7 0.4 0.5 0.5
0
0.6 0.4 0.4 0.7 0.5 4.7 0.8
[1] 2z6q.a 0.7 0.5 0.6 0.6 0.6
0
0.5 0.5 0.8 0.6 4.9 0.9
[1] 2z6u.a 0.6 0.2 0.4 0.5 0.4 0.5
0
0.2 0.7 0.4 4.8 0.8
[1] 2zcj.a 0.6 0.3 0.5 0.5 0.4 0.5 0.2
0
0.6 0.4 4.7 0.8
[1] 3eeo.a 0.7 0.6 0.6 0.6 0.7 0.8 0.7 0.6
0
0.7 4.7 0.7
[1] 4mht.a 0.6 0.4 0.6 0.6 0.5 0.6 0.4 0.4 0.7
0
4.7 0.7
[1] 5lod.b 4.7 4.7 4.8 4.7 4.7 4.9 4.8 4.7 4.7 4.7
0
4.7
[1] 6mht.a 0.9 0.9 0.8 0.8 0.8 0.9 0.8 0.8 0.7 0.7 4.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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