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SMTL ID : 3dl0.2
(1 other biounit)
Crystal structure of adenylate kinase variant AKlse3
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.58 Å
Oligo State
monomer
Ligands
1 x
ZN
:
ZINC ION
(Non-covalent)
ZN.1:
4 residues within 4Å:
Chain A:
C.130
,
C.133
,
C.150
,
D.153
4
PLIP interactions
:
4 interactions with chain A
Metal complexes:
A:C.130
,
A:C.133
,
A:C.150
,
A:D.153
1 x
MG
:
MAGNESIUM ION
(Non-functional Binders)
MG.2:
1 residues within 4Å:
Ligands:
AP5.3
No protein-ligand interaction detected (PLIP)
1 x
AP5
:
BIS(ADENOSINE)-5'-PENTAPHOSPHATE
(Non-covalent)
AP5.3:
34 residues within 4Å:
Chain A:
P.9
,
G.10
,
A.11
,
G.12
,
K.13
,
G.14
,
T.15
,
T.31
,
G.32
,
F.35
,
R.36
,
I.53
,
E.57
,
L.58
,
V.59
,
T.64
,
G.85
,
F.86
,
R.88
,
Q.92
,
R.123
,
L.124
,
R.127
,
T.136
,
Y.137
,
H.138
,
F.141
,
R.160
,
R.171
,
G.197
,
Q.199
,
D.200
,
I.201
Ligands:
MG.2
47
PLIP interactions
:
47 interactions with chain A
Hydrogen bonds:
A:G.10
,
A:G.12
,
A:K.13
,
A:G.14
,
A:T.15
,
A:T.15
,
A:T.31
,
A:E.57
,
A:V.59
,
A:T.64
,
A:R.88
,
A:Q.92
,
A:Q.92
,
A:R.123
,
A:R.123
,
A:Y.137
,
A:Q.199
Water bridges:
A:A.11
,
A:A.11
,
A:K.13
,
A:S.30
,
A:T.31
,
A:G.32
,
A:R.88
,
A:R.123
,
A:R.127
,
A:R.127
,
A:T.136
,
A:N.142
,
A:R.160
,
A:N.175
,
A:N.175
Salt bridges:
A:K.13
,
A:K.13
,
A:K.13
,
A:R.36
,
A:R.88
,
A:R.88
,
A:R.127
,
A:R.127
,
A:R.160
,
A:R.160
,
A:R.171
,
A:R.171
pi-Stacking:
A:F.35
pi-Cation interactions:
A:R.88
,
A:R.123
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Moon, S. et al., Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases. Proteins (2014)
Release Date
2009-06-09
Peptides
Adenylate kinase:
A
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
B
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Adenylate kinase
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3dl0.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
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