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SMTL ID : 3gdl.1
Crystal structure of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.65 Å
Oligo State
homo-dimer
Ligands
2 x
UP6
:
6-AZA URIDINE 5'-MONOPHOSPHATE
(Non-covalent)
UP6.1:
16 residues within 4Å:
Chain A:
S.35
,
D.37
,
K.59
,
H.61
,
D.91
,
K.93
,
L.153
,
S.154
,
P.202
,
Q.215
,
Y.217
,
G.234
,
R.235
Chain B:
D.96
,
I.97
,
T.100
17
PLIP interactions
:
15 interactions with chain A
,
2 interactions with chain B
Hydrogen bonds:
A:S.35
,
A:D.37
,
A:K.59
,
A:D.91
,
A:K.93
,
A:S.154
,
A:Q.215
,
A:G.234
,
A:R.235
,
B:D.96
,
B:T.100
Water bridges:
A:E.152
,
A:Q.185
,
A:G.203
,
A:V.204
,
A:G.236
Salt bridges:
A:R.235
UP6.2:
16 residues within 4Å:
Chain A:
D.96
,
I.97
,
T.100
Chain B:
S.35
,
D.37
,
K.59
,
H.61
,
D.91
,
K.93
,
L.153
,
S.154
,
P.202
,
Q.215
,
Y.217
,
G.234
,
R.235
17
PLIP interactions
:
14 interactions with chain B
,
3 interactions with chain A
Hydrogen bonds:
B:S.35
,
B:K.59
,
B:K.93
,
B:S.154
,
B:Q.215
,
B:Y.217
,
B:G.234
,
B:R.235
,
A:D.96
,
A:T.100
,
A:T.100
Water bridges:
B:D.37
,
B:Q.185
,
B:G.203
,
B:V.204
,
B:G.236
Salt bridges:
B:R.235
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Chan, K.K. et al., Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization. Biochemistry (2009)
Release Date
2009-06-23
Peptides
Orotidine 5'-phosphate decarboxylase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Orotidine 5'-phosphate decarboxylase
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