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SMTL ID : 3geh.1
Crystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 3.20 Å
Oligo State
homo-dimer
Ligands
2 x
GDP
:
GUANOSINE-5'-DIPHOSPHATE
(Non-covalent)
GDP.1:
15 residues within 4Å:
Chain A:
R.232
,
N.234
,
V.235
,
G.236
,
K.237
,
S.238
,
S.239
,
N.338
,
K.339
,
D.341
,
L.342
,
A.364
,
A.365
,
A.366
Ligands:
ZN.4
14
PLIP interactions
:
14 interactions with chain A
Hydrogen bonds:
A:N.234
,
A:V.235
,
A:G.236
,
A:K.237
,
A:S.238
,
A:S.239
,
A:S.239
,
A:N.338
,
A:K.339
,
A:K.339
,
A:A.365
,
A:A.366
Salt bridges:
A:K.237
,
A:D.341
GDP.5:
15 residues within 4Å:
Chain B:
R.232
,
N.234
,
V.235
,
G.236
,
K.237
,
S.238
,
S.239
,
N.338
,
K.339
,
D.341
,
L.342
,
A.364
,
A.365
,
A.366
Ligands:
ZN.8
14
PLIP interactions
:
14 interactions with chain B
Hydrogen bonds:
B:N.234
,
B:V.235
,
B:G.236
,
B:K.237
,
B:S.238
,
B:S.239
,
B:S.239
,
B:N.338
,
B:K.339
,
B:K.339
,
B:A.365
,
B:A.366
Salt bridges:
B:K.237
,
B:D.341
2 x
FON
:
N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid
(Non-covalent)
FON.2:
15 residues within 4Å:
Chain A:
R.28
,
R.81
,
S.82
,
Y.83
,
R.85
,
E.90
,
R.129
Chain B:
S.23
,
V.24
,
Y.57
,
E.71
,
L.73
,
H.92
,
C.93
,
H.94
15
PLIP interactions
:
7 interactions with chain A
,
8 interactions with chain B
Hydrophobic interactions:
A:R.81
,
B:Y.57
,
B:Y.57
,
B:Y.57
,
B:L.73
Hydrogen bonds:
A:R.28
,
A:S.82
,
B:E.71
,
B:H.92
,
B:H.92
,
B:H.92
Salt bridges:
A:R.81
,
A:R.85
,
A:E.90
,
A:R.129
FON.6:
15 residues within 4Å:
Chain A:
S.23
,
V.24
,
Y.57
,
E.71
,
L.73
,
H.92
,
C.93
,
H.94
Chain B:
R.28
,
R.81
,
S.82
,
Y.83
,
R.85
,
E.90
,
R.129
15
PLIP interactions
:
7 interactions with chain B
,
8 interactions with chain A
Hydrophobic interactions:
B:R.81
,
A:Y.57
,
A:Y.57
,
A:Y.57
,
A:L.73
Hydrogen bonds:
B:R.28
,
B:S.82
,
A:E.71
,
A:H.92
,
A:H.92
,
A:H.92
Salt bridges:
B:R.81
,
B:R.85
,
B:E.90
,
B:R.129
4 x
ZN
:
ZINC ION
(Non-covalent)
ZN.3:
1 residues within 4Å:
Chain A:
E.352
2
PLIP interactions
:
2 interactions with chain A
Metal complexes:
A:E.352
,
A:E.352
ZN.4:
2 residues within 4Å:
Chain A:
S.238
Ligands:
GDP.1
No protein-ligand interaction detected (PLIP)
ZN.7:
1 residues within 4Å:
Chain B:
E.352
2
PLIP interactions
:
2 interactions with chain B
Metal complexes:
B:E.352
,
B:E.352
ZN.8:
2 residues within 4Å:
Chain B:
S.238
Ligands:
GDP.5
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Meyer, S. et al., Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy. Plos Biol. (2009)
Release Date
2009-10-27
Peptides
tRNA modification GTPase mnmE:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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