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SMTL ID : 4rdi.1
(1 other biounit)
Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.95 Å
Oligo State
homo-dimer
Ligands
2 x
ATP
:
ADENOSINE-5'-TRIPHOSPHATE
(Non-covalent)
ATP.1:
19 residues within 4Å:
Chain A:
V.56
,
G.57
,
I.58
,
G.59
,
G.60
,
I.80
,
D.81
,
D.83
,
N.89
,
R.92
,
Q.93
,
K.105
,
F.128
,
V.129
,
A.148
,
I.149
,
D.150
,
S.151
,
P.154
27
PLIP interactions
:
27 interactions with chain A
Hydrogen bonds:
A:I.58
,
A:I.58
,
A:G.60
,
A:D.83
,
A:D.83
,
A:T.88
,
A:N.89
,
A:Q.93
,
A:V.129
,
A:V.129
,
A:D.150
Water bridges:
A:V.61
,
A:V.61
,
A:V.61
,
A:N.89
,
A:R.92
,
A:R.92
,
A:R.92
,
A:K.105
,
A:D.150
,
A:D.150
,
A:S.151
Salt bridges:
A:R.92
,
A:R.92
,
A:R.92
,
A:K.105
,
A:K.105
ATP.3:
19 residues within 4Å:
Chain B:
V.56
,
G.57
,
I.58
,
G.59
,
G.60
,
I.80
,
D.81
,
D.83
,
N.89
,
R.92
,
Q.93
,
K.105
,
F.128
,
V.129
,
A.148
,
I.149
,
D.150
,
S.151
,
P.154
25
PLIP interactions
:
25 interactions with chain B
Hydrogen bonds:
B:I.58
,
B:I.58
,
B:G.60
,
B:D.83
,
B:D.83
,
B:N.89
,
B:Q.93
,
B:K.105
,
B:V.129
,
B:V.129
Water bridges:
B:G.59
,
B:V.61
,
B:D.83
,
B:N.89
,
B:R.92
,
B:R.92
,
B:R.92
,
B:R.92
,
B:S.151
,
B:S.151
Salt bridges:
B:R.92
,
B:R.92
,
B:R.92
,
B:K.105
,
B:K.105
2 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.2:
8 residues within 4Å:
Chain A:
C.162
,
R.163
,
I.167
,
P.168
,
L.169
,
G.220
,
V.221
,
D.222
6
PLIP interactions
:
6 interactions with chain A
Hydrogen bonds:
A:C.162
,
A:I.167
,
A:L.169
,
A:D.222
,
A:D.222
Water bridges:
A:K.166
GOL.4:
8 residues within 4Å:
Chain B:
C.162
,
R.163
,
I.167
,
P.168
,
L.169
,
G.220
,
V.221
,
D.222
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:C.162
,
B:I.167
,
B:L.169
,
B:D.222
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Kim, S. et al., The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity. J.Mol.Biol. (2015)
Release Date
2015-08-05
Peptides
tRNA threonylcarbamoyladenosine dehydratase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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tRNA threonylcarbamoyladenosine dehydratase
Related Entries With Identical Sequence
4rdh.1
|
4rdh.2
|
4rdi.2
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
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