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SMTL ID : 3iji.2
(1 other biounit)
Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with L-Ala-D-Glu; nonproductive substrate binding.
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.60 Å
Oligo State
homo-dimer
Ligands
2 x
ALA
:
ALANINE
(Non-covalent)
ALA.1:
8 residues within 4Å:
Chain A:
F.16
,
K.153
,
K.155
,
C.281
,
D.303
,
D.305
,
L.309
Ligands:
DGL.2
6
PLIP interactions
:
6 interactions with chain A
Hydrophobic interactions:
A:L.309
Hydrogen bonds:
A:K.153
,
A:K.155
,
A:D.305
Water bridges:
A:T.129
,
A:T.129
ALA.4:
9 residues within 4Å:
Chain B:
F.16
,
K.153
,
K.155
,
C.281
,
M.282
,
D.303
,
D.305
,
L.309
Ligands:
DGL.5
6
PLIP interactions
:
6 interactions with chain B
Hydrophobic interactions:
B:F.16
,
B:L.309
Hydrogen bonds:
B:K.153
,
B:K.155
,
B:D.305
Water bridges:
B:T.129
2 x
DGL
:
D-GLUTAMIC ACID
(Non-covalent)
DGL.2:
10 residues within 4Å:
Chain A:
F.16
,
V.18
,
R.23
,
P.47
,
Y.49
,
K.253
,
C.281
,
M.282
,
T.283
Ligands:
ALA.1
15
PLIP interactions
:
15 interactions with chain A
Hydrophobic interactions:
A:F.16
Hydrogen bonds:
A:C.281
,
A:C.281
,
A:T.283
Water bridges:
A:Y.49
,
A:D.179
,
A:D.179
,
A:N.251
,
A:K.253
,
A:K.253
,
A:C.281
,
A:C.281
Salt bridges:
A:R.23
,
A:K.153
,
A:K.253
DGL.5:
10 residues within 4Å:
Chain B:
F.16
,
V.18
,
R.23
,
P.47
,
Y.49
,
K.253
,
C.281
,
M.282
,
T.283
Ligands:
ALA.4
19
PLIP interactions
:
19 interactions with chain B
Hydrophobic interactions:
B:F.16
,
B:V.18
Hydrogen bonds:
B:Y.49
,
B:C.281
,
B:C.281
,
B:T.283
Water bridges:
B:K.153
,
B:K.153
,
B:N.181
,
B:N.251
,
B:N.251
,
B:K.253
,
B:K.253
,
B:K.253
,
B:C.281
,
B:C.281
Salt bridges:
B:R.23
,
B:K.153
,
B:K.253
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.3:
4 residues within 4Å:
Chain A:
D.179
,
E.206
,
D.231
,
K.253
6
PLIP interactions
:
3 interactions with chain A
,
3 Ligand-Water interactions
Metal complexes:
A:D.179
,
A:E.206
,
A:D.231
,
H
2
O.3
,
H
2
O.4
,
H
2
O.6
MG.6:
4 residues within 4Å:
Chain B:
D.179
,
E.206
,
D.231
,
K.253
6
PLIP interactions
:
3 interactions with chain B
,
3 Ligand-Water interactions
Metal complexes:
B:D.179
,
B:E.206
,
B:D.231
,
H
2
O.17
,
H
2
O.20
,
H
2
O.21
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Lukk, T. et al., Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily. Proc.Natl.Acad.Sci.USA (2012)
Release Date
2010-07-21
Peptides
Muconate cycloisomerase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Toggle Identical (AB)
Related Entries With Identical Sequence
3iji.1
|
3ijl.1
|
3ijl.2
|
3ijq.1
|
3ijq.2
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