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SMTL ID : 2zz4.1
Covalent complex of orotidine monophosphate decarboxylase D75N mutant from M. thermoautotrophicum with 6-cyano-UMP
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.67 Å
Oligo State
homo-dimer
Ligands
2 x
6CN
:
6-cyanouridine 5'-phosphate
(Covalent)
6CN.1:
16 residues within 4Å:
Chain A:
A.21
,
D.23
,
K.45
,
D.73
,
K.75
,
M.129
,
S.130
,
P.183
,
V.185
,
Q.188
,
V.204
,
G.205
,
R.206
Chain B:
N.78
,
I.79
,
T.82
18
PLIP interactions
:
16 interactions with chain A
,
2 interactions with chain B
Hydrophobic interactions:
A:K.75
,
A:P.183
Hydrogen bonds:
A:D.23
,
A:K.45
,
A:K.75
,
A:S.130
,
A:S.130
,
A:S.130
,
A:Q.188
,
A:G.205
,
A:R.206
,
B:N.78
,
B:T.82
Water bridges:
A:G.184
,
A:G.184
,
A:G.184
,
A:S.207
Salt bridges:
A:R.206
6CN.3:
16 residues within 4Å:
Chain A:
N.78
,
I.79
,
T.82
Chain B:
A.21
,
D.23
,
K.45
,
D.73
,
K.75
,
M.129
,
S.130
,
P.183
,
V.185
,
Q.188
,
V.204
,
G.205
,
R.206
21
PLIP interactions
:
18 interactions with chain B
,
3 interactions with chain A
Hydrophobic interactions:
B:K.75
,
B:P.183
Hydrogen bonds:
B:D.23
,
B:K.45
,
B:D.73
,
B:K.75
,
B:S.130
,
B:S.130
,
B:S.130
,
B:Q.188
,
B:G.205
,
B:R.206
,
A:N.78
,
A:T.82
,
A:T.82
Water bridges:
B:D.23
,
B:G.184
,
B:G.184
,
B:G.184
,
B:S.207
Salt bridges:
B:R.206
2 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.2:
3 residues within 4Å:
Chain A:
T.162
,
P.164
,
G.189
No protein-ligand interaction detected (PLIP)
GOL.4:
3 residues within 4Å:
Chain B:
T.162
,
P.164
,
G.189
No protein-ligand interaction detected (PLIP)
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Fujihashi, M. et al., Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase. J.Mol.Biol. (2009)
Release Date
2009-03-24
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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3wjz.1
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