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SMTL ID : 4df1.1
Crystal structure of orotidine 5'-monophosphate decarboxylase from Thermoproteus neutrophilus complexed with inhibitor BMP
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.90 Å
Oligo State
homo-dimer
Ligands
2 x
BMP
:
6-HYDROXYURIDINE-5'-PHOSPHATE
(Non-covalent)
BMP.1:
18 residues within 4Å:
Chain A:
A.10
,
D.12
,
K.33
,
D.59
,
K.61
,
M.106
,
T.107
,
P.155
,
I.157
,
Q.160
,
I.176
,
V.177
,
G.178
,
R.179
Chain B:
D.64
,
V.65
,
H.67
,
V.68
17
PLIP interactions
:
16 interactions with chain A
,
1 interactions with chain B
Hydrophobic interactions:
A:P.155
Hydrogen bonds:
A:D.12
,
A:D.12
,
A:K.33
,
A:D.59
,
A:K.61
,
A:T.107
,
A:T.107
,
A:I.157
,
A:Q.160
,
A:G.178
,
A:R.179
Water bridges:
A:G.156
,
A:G.156
,
A:Y.180
Salt bridges:
A:R.179
,
B:H.67
BMP.3:
17 residues within 4Å:
Chain A:
D.64
,
V.65
,
H.67
,
V.68
Chain B:
A.10
,
D.12
,
K.33
,
D.59
,
K.61
,
M.106
,
T.107
,
P.155
,
I.157
,
Q.160
,
V.177
,
G.178
,
R.179
19
PLIP interactions
:
18 interactions with chain B
,
1 interactions with chain A
Hydrophobic interactions:
B:P.155
Hydrogen bonds:
B:D.12
,
B:K.33
,
B:D.59
,
B:K.61
,
B:T.107
,
B:T.107
,
B:T.107
,
B:I.157
,
B:Q.160
,
B:G.178
,
B:R.179
Water bridges:
B:D.12
,
B:K.33
,
B:G.156
,
B:R.179
,
B:Y.180
Salt bridges:
B:R.179
,
A:H.67
2 x
NI
:
NICKEL (II) ION
(Non-covalent)
NI.2:
4 residues within 4Å:
Chain A:
C.82
,
C.83
,
R.127
,
P.202
2
PLIP interactions
:
2 interactions with chain A
Metal complexes:
A:C.82
,
A:C.83
NI.4:
4 residues within 4Å:
Chain B:
C.82
,
C.83
,
R.127
,
P.202
2
PLIP interactions
:
2 interactions with chain B
Metal complexes:
B:C.82
,
B:C.83
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Fedorov, A.A. et al., Crystal structure of orotidine 5'-monophosphate decarboxylase from Thermoproteus neutrophilus complexed with inhibitor BMP. To be Published
Release Date
2013-01-23
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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