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SMTL ID : 6c4t.1
Staphylopine dehydrogenase (SaODH) - NADP+ bound
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.49 Å
Oligo State
homo-dimer
Ligands
2 x
NA7
:
[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4S)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE
(Non-covalent)
NA7.1:
21 residues within 4Å:
Chain A:
G.26
,
T.27
,
G.28
,
P.29
,
V.30
,
A.31
,
R.51
,
S.55
,
K.57
,
S.58
,
V.95
,
A.108
,
C.109
,
T.110
,
A.111
,
A.113
,
D.116
,
T.117
,
S.136
,
R.374
,
E.378
19
PLIP interactions
:
19 interactions with chain A
Hydrogen bonds:
A:T.27
,
A:T.27
,
A:G.28
,
A:V.30
,
A:S.55
,
A:S.58
,
A:S.58
,
A:S.58
,
A:S.58
,
A:A.108
,
A:D.116
,
A:S.136
,
A:R.374
Salt bridges:
A:R.51
,
A:K.57
,
A:K.57
,
A:R.374
,
A:R.374
pi-Cation interactions:
A:R.51
NA7.3:
21 residues within 4Å:
Chain B:
G.26
,
T.27
,
G.28
,
P.29
,
V.30
,
A.31
,
R.51
,
S.55
,
K.57
,
S.58
,
V.95
,
A.108
,
C.109
,
T.110
,
A.111
,
A.113
,
D.116
,
T.117
,
S.136
,
R.374
,
E.378
19
PLIP interactions
:
19 interactions with chain B
Hydrogen bonds:
B:T.27
,
B:T.27
,
B:G.28
,
B:V.30
,
B:S.55
,
B:S.58
,
B:S.58
,
B:S.58
,
B:S.58
,
B:A.108
,
B:D.116
,
B:S.136
,
B:R.374
Salt bridges:
B:R.51
,
B:K.57
,
B:K.57
,
B:R.374
,
B:R.374
pi-Cation interactions:
B:R.51
2 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.2:
8 residues within 4Å:
Chain A:
Q.119
,
Q.120
,
L.121
,
S.122
,
L.123
,
L.126
,
F.148
,
F.152
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:Q.119
GOL.4:
8 residues within 4Å:
Chain B:
Q.119
,
Q.120
,
L.121
,
S.122
,
L.123
,
L.126
,
F.148
,
F.152
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:Q.119
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
McFarlane, J.S. et al., Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase. J. Biol. Chem. (2018)
Release Date
2018-04-11
Peptides
Staphylopine dehydrogenase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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Staphylopine dehydrogenase
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