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SMTL ID : 6ywt.1
Human OMPD-domain of UMPS (K314AcK) in complex with 6-hydroxy-UMP at 1.05 Angstroms resolution
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.05 Å
Oligo State
homo-dimer
Ligands
2 x
BMP
:
6-HYDROXYURIDINE-5'-PHOSPHATE
(Non-covalent)
BMP.1:
18 residues within 4Å:
Chain A:
S.37
,
D.39
,
K.61
,
H.63
,
D.92
,
K.94
,
M.151
,
S.152
,
I.181
,
P.197
,
Q.210
,
Y.212
,
V.229
,
G.230
,
R.231
Chain B:
D.97
,
I.98
,
T.101
22
PLIP interactions
:
20 interactions with chain A
,
2 interactions with chain B
Hydrophobic interactions:
A:I.181
,
A:P.197
Hydrogen bonds:
A:S.37
,
A:D.39
,
A:D.39
,
A:K.61
,
A:D.92
,
A:S.152
,
A:S.152
,
A:S.152
,
A:Q.210
,
A:Y.212
,
A:Y.212
,
A:Y.212
,
A:G.230
,
A:R.231
,
B:T.101
,
B:T.101
Water bridges:
A:G.198
,
A:G.198
,
A:Q.200
Salt bridges:
A:R.231
BMP.4:
18 residues within 4Å:
Chain A:
D.97
,
I.98
,
T.101
Chain B:
S.37
,
D.39
,
K.61
,
H.63
,
D.92
,
K.94
,
M.151
,
S.152
,
I.181
,
P.197
,
Q.210
,
Y.212
,
V.229
,
G.230
,
R.231
19
PLIP interactions
:
18 interactions with chain B
,
1 interactions with chain A
Hydrophobic interactions:
B:I.181
,
B:P.197
Hydrogen bonds:
B:S.37
,
B:D.39
,
B:K.61
,
B:D.92
,
B:S.152
,
B:S.152
,
B:S.152
,
B:Q.210
,
B:Y.212
,
B:Y.212
,
B:G.230
,
B:R.231
,
A:T.101
Water bridges:
B:G.198
,
B:G.198
,
B:Q.200
Salt bridges:
B:R.231
4 x
PRO
:
PROLINE
(Non-covalent)
PRO.2:
2 residues within 4Å:
Chain A:
L.201
,
A.203
3
PLIP interactions
:
1 interactions with chain A
,
2 Ligand-Ligand interactions
Water bridges:
A:S.214
Hydrogen bonds:
P.2
,
P.2
PRO.3:
6 residues within 4Å:
Chain A:
Q.200
,
E.202
,
A.203
,
G.204
,
G.205
,
Y.212
4
PLIP interactions
:
1 Ligand-Ligand interactions
,
3 interactions with chain A
Hydrogen bonds:
P.3
,
A:A.203
,
A:G.205
Hydrophobic interactions:
A:Y.212
PRO.5:
2 residues within 4Å:
Chain B:
L.201
,
A.203
3
PLIP interactions
:
1 interactions with chain B
,
2 Ligand-Ligand interactions
Water bridges:
B:S.214
Hydrogen bonds:
P.5
,
P.5
PRO.6:
6 residues within 4Å:
Chain B:
Q.200
,
E.202
,
A.203
,
G.204
,
G.205
,
Y.212
4
PLIP interactions
:
3 interactions with chain B
,
1 Ligand-Ligand interactions
Hydrophobic interactions:
B:Y.212
Hydrogen bonds:
B:A.203
,
B:G.205
,
P.6
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Rindfleisch, S. et al., Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis. Nat Catal (2022)
Release Date
2022-02-23
Peptides
Uridine 5'-monophosphate synthase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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Secondary Structure
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Uridine 5'-monophosphate synthase
Toggle Identical (AB)
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