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SMTL ID : 6a9a.1
Ternary complex crystal structure of dCH with dCMP and THF
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.90 Å
Oligo State
homo-dimer
Ligands
2 x
IOD
:
IODIDE ION
(Non-functional Binders)
IOD.1:
2 residues within 4Å:
Chain A:
K.72
,
Q.83
Ligand excluded by PLIP
IOD.4:
2 residues within 4Å:
Chain B:
K.72
,
Q.83
Ligand excluded by PLIP
2 x
DCM
:
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
(Non-covalent)
DCM.2:
15 residues within 4Å:
Chain A:
K.28
,
Y.96
,
S.148
,
M.167
,
R.168
,
S.169
,
N.170
,
D.171
,
G.175
,
N.179
,
H.216
,
Y.218
Chain B:
R.123
,
R.124
Ligands:
THG.3
15
PLIP interactions
:
11 interactions with chain A
,
4 interactions with chain B
Hydrogen bonds:
A:Y.96
,
A:S.169
,
A:N.170
,
A:D.171
,
A:N.179
,
A:N.179
,
A:H.216
,
A:Y.218
Water bridges:
A:T.149
,
B:R.124
,
B:R.124
Salt bridges:
A:K.28
,
A:R.168
,
B:R.123
,
B:R.124
DCM.5:
15 residues within 4Å:
Chain A:
R.123
,
R.124
Chain B:
K.28
,
Y.96
,
S.148
,
M.167
,
R.168
,
S.169
,
N.170
,
D.171
,
G.175
,
N.179
,
H.216
,
Y.218
Ligands:
THG.6
15
PLIP interactions
:
11 interactions with chain B
,
4 interactions with chain A
Hydrogen bonds:
B:Y.96
,
B:S.169
,
B:N.170
,
B:D.171
,
B:N.179
,
B:N.179
,
B:H.216
,
B:Y.218
Water bridges:
B:T.149
,
A:R.124
,
A:R.124
Salt bridges:
B:K.28
,
B:R.168
,
A:R.123
,
A:R.124
2 x
THG
:
(6S)-5,6,7,8-TETRAHYDROFOLATE
(Non-covalent)
THG.3:
14 residues within 4Å:
Chain A:
K.28
,
N.53
,
Y.56
,
R.59
,
P.79
,
I.81
,
W.82
,
V.85
,
F.174
,
R.177
,
N.178
,
Y.218
,
R.220
Ligands:
DCM.2
20
PLIP interactions
:
20 interactions with chain A
Hydrophobic interactions:
A:Y.56
,
A:P.79
,
A:I.81
,
A:F.174
Hydrogen bonds:
A:K.28
,
A:N.53
,
A:Y.218
,
A:Y.218
,
A:R.220
Water bridges:
A:K.28
,
A:K.28
,
A:S.144
,
A:D.171
,
A:R.177
,
A:R.177
,
A:N.178
,
A:Y.218
,
A:Y.218
Salt bridges:
A:R.59
,
A:R.177
THG.6:
14 residues within 4Å:
Chain B:
K.28
,
N.53
,
Y.56
,
R.59
,
P.79
,
I.81
,
W.82
,
V.85
,
F.174
,
R.177
,
N.178
,
Y.218
,
R.220
Ligands:
DCM.5
20
PLIP interactions
:
20 interactions with chain B
Hydrophobic interactions:
B:Y.56
,
B:P.79
,
B:I.81
,
B:F.174
Hydrogen bonds:
B:K.28
,
B:N.53
,
B:Y.218
,
B:Y.218
,
B:R.220
Water bridges:
B:K.28
,
B:K.28
,
B:S.144
,
B:D.171
,
B:R.177
,
B:R.177
,
B:N.178
,
B:Y.218
,
B:Y.218
Salt bridges:
B:R.59
,
B:R.177
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Park, S.H. et al., A cytosine modification mechanism revealed by the structure of a ternary complex of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate. Iucrj (2019)
Release Date
2019-01-02
Peptides
Deoxycytidylate 5-hydroxymethyltransferase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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