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SMTL ID : 5fwa.1
Crystal Structure of Mus musculus Protein Arginine Methyltransferase 2 with CP1
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.80 Å
Oligo State
homo-dimer
Ligands
2 x
J7C
:
9-(6-carbamimidamido-5,6-dideoxy-beta-D-ribo-hexofuranosyl)-9H-purin-6-amine
(Non-covalent)
J7C.1:
20 residues within 4Å:
Chain A:
Y.115
,
F.116
,
Y.119
,
H.125
,
G.158
,
G.160
,
E.181
,
A.182
,
S.183
,
Q.207
,
K.208
,
V.209
,
E.210
,
E.224
,
W.225
,
M.226
,
G.227
,
E.233
,
M.235
,
S.238
15
PLIP interactions
:
15 interactions with chain A
Hydrophobic interactions:
A:Y.119
Hydrogen bonds:
A:H.125
,
A:G.158
,
A:A.182
,
A:S.183
,
A:V.209
,
A:E.210
,
A:E.224
,
A:M.226
,
A:S.238
Water bridges:
A:T.228
,
A:R.416
Salt bridges:
A:E.224
,
A:E.233
pi-Stacking:
A:F.116
J7C.9:
20 residues within 4Å:
Chain B:
Y.115
,
F.116
,
Y.119
,
H.125
,
G.158
,
G.160
,
E.181
,
A.182
,
S.183
,
Q.207
,
K.208
,
V.209
,
E.210
,
E.224
,
W.225
,
M.226
,
G.227
,
E.233
,
M.235
,
S.238
17
PLIP interactions
:
17 interactions with chain B
Hydrophobic interactions:
B:Y.119
Hydrogen bonds:
B:H.125
,
B:G.158
,
B:A.182
,
B:S.183
,
B:V.209
,
B:E.210
,
B:E.224
,
B:M.226
,
B:S.238
Water bridges:
B:Y.119
,
B:Y.119
,
B:T.228
,
B:R.416
Salt bridges:
B:E.224
,
B:E.233
pi-Stacking:
B:F.116
2 x
PG4
:
TETRAETHYLENE GLYCOL
(Non-functional Binders)
PG4.2:
6 residues within 4Å:
Chain A:
K.150
,
D.151
,
K.152
,
D.219
,
D.250
,
L.363
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:K.152
,
A:D.250
PG4.10:
6 residues within 4Å:
Chain B:
K.150
,
D.151
,
K.152
,
D.219
,
D.250
,
L.363
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:K.152
,
B:D.250
2 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.3:
4 residues within 4Å:
Chain A:
G.375
,
P.376
,
L.377
,
H.378
Ligand excluded by PLIP
CL.11:
4 residues within 4Å:
Chain B:
G.375
,
P.376
,
L.377
,
H.378
Ligand excluded by PLIP
6 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.4:
2 residues within 4Å:
Chain A:
R.300
,
W.445
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:R.300
,
A:W.446
EDO.5:
4 residues within 4Å:
Chain A:
P.376
,
L.377
,
H.378
,
T.380
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:L.377
,
A:T.380
Water bridges:
A:T.380
EDO.6:
4 residues within 4Å:
Chain A:
Q.111
,
Y.115
,
F.232
,
H.417
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:Q.111
Water bridges:
A:S.118
EDO.12:
2 residues within 4Å:
Chain B:
R.300
,
W.445
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:R.300
,
B:W.446
EDO.13:
4 residues within 4Å:
Chain B:
P.376
,
L.377
,
H.378
,
T.380
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:L.377
Water bridges:
B:T.380
EDO.14:
4 residues within 4Å:
Chain B:
Q.111
,
Y.115
,
F.232
,
H.417
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:Q.111
Water bridges:
B:S.118
4 x
CA
:
CALCIUM ION
(Non-covalent)
(Non-functional Binders)
CA.7:
2 residues within 4Å:
Chain A:
G.197
,
D.200
5
PLIP interactions
:
3 interactions with chain A
,
2 Ligand-Water interactions
Metal complexes:
A:G.197
,
A:D.200
,
A:D.200
,
H
2
O.4
,
H
2
O.4
CA.8:
0 residues within 4Å:
(No contacts)
No protein-ligand interaction detected (PLIP)
CA.15:
2 residues within 4Å:
Chain B:
G.197
,
D.200
5
PLIP interactions
:
3 interactions with chain B
,
2 Ligand-Water interactions
Metal complexes:
B:G.197
,
B:D.200
,
B:D.200
,
H
2
O.16
,
H
2
O.16
CA.16:
0 residues within 4Å:
(No contacts)
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Cura, V. et al., Structural studies of protein arginine methyltransferase 2 reveal its interactions with potential substrates and inhibitors. FEBS J. (2017)
Release Date
2016-11-09
Peptides
PROTEIN ARGININE N-METHYLTRANSFERASE 2:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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PROTEIN ARGININE N-METHYLTRANSFERASE 2
Toggle Identical (AB)
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5ful.1
|
5fwd.1
|
5jmq.1
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