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SMTL ID : 5trd.1
Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.85 Å
Oligo State
homo-dimer
Ligands
2 x
CTP
:
CYTIDINE-5'-TRIPHOSPHATE
(Non-covalent)
CTP.1:
18 residues within 4Å:
Chain A:
S.103
,
G.104
,
M.105
,
G.106
,
E.107
,
G.108
,
R.109
,
Y.130
,
G.132
,
T.133
,
L.134
,
N.135
,
S.200
,
K.202
,
Y.203
,
L.204
,
R.205
Ligands:
NA.2
23
PLIP interactions
:
23 interactions with chain A
Hydrophobic interactions:
A:Y.130
Hydrogen bonds:
A:G.104
,
A:M.105
,
A:G.106
,
A:E.107
,
A:G.108
,
A:R.109
,
A:Y.130
,
A:T.133
,
A:N.135
,
A:N.135
,
A:S.200
,
A:K.202
,
A:L.204
,
A:R.205
,
A:R.205
,
A:R.205
Water bridges:
A:T.102
,
A:R.109
,
A:T.133
,
A:T.133
,
A:N.135
,
A:Y.203
CTP.3:
18 residues within 4Å:
Chain B:
S.103
,
G.104
,
M.105
,
G.106
,
E.107
,
G.108
,
R.109
,
Y.130
,
G.132
,
T.133
,
L.134
,
N.135
,
S.200
,
K.202
,
Y.203
,
L.204
,
R.205
Ligands:
NA.4
16
PLIP interactions
:
16 interactions with chain B
Hydrophobic interactions:
B:Y.130
Hydrogen bonds:
B:G.104
,
B:M.105
,
B:G.106
,
B:E.107
,
B:G.108
,
B:R.109
,
B:T.133
,
B:T.133
,
B:N.135
,
B:S.200
,
B:K.202
,
B:L.204
,
B:R.205
,
B:R.205
,
B:R.205
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.2:
4 residues within 4Å:
Chain A:
T.133
,
N.135
,
E.197
Ligands:
CTP.1
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:T.133
,
A:N.135
,
A:E.197
Water bridges:
A:N.135
NA.4:
4 residues within 4Å:
Chain B:
T.133
,
N.135
,
E.197
Ligands:
CTP.3
6
PLIP interactions
:
6 interactions with chain B
Hydrogen bonds:
B:T.133
,
B:T.133
,
B:N.135
,
B:E.197
Water bridges:
B:G.108
,
B:N.135
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Vetting, M.W. et al., Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator. To be published
Release Date
2016-11-23
Peptides
Riboflavin kinase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
Export Alignment
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Secondary Structure
None
DSSP
PSIPRED
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Colour Scheme
Fade Mismatches
Enhance Mismatches
Chain
Unique Chain
Rainbow
2° Structure
Bfactor
Bfactor Range
SOA
Entropy
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Size
Charged
Polar
Proline
Ser/Thr
Cysteine
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Aromatic
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3D Viewer
NGL
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2D
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Riboflavin kinase
Related Entries With Identical Sequence
3cta.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
Resolution
Low
Medium
High
Extreme