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SMTL ID : 3eib.1
Crystal structure of K270N variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.85 Å
Oligo State
homo-dimer
Ligands
2 x
PLP
:
PYRIDOXAL-5'-PHOSPHATE
(Non-covalent)
PLP.1:
15 residues within 4Å:
Chain A:
G.127
,
A.128
,
K.129
,
Y.152
,
C.205
,
N.209
,
D.237
,
Y.240
,
S.267
,
S.269
,
N.270
,
R.278
Chain B:
Y.94
,
N.309
Ligands:
SO4.2
17
PLIP interactions
:
2 interactions with chain B
,
15 interactions with chain A
Hydrogen bonds:
B:Y.94
,
B:N.309
,
A:A.128
,
A:K.129
,
A:N.209
,
A:S.267
,
A:S.267
,
A:S.269
,
A:N.270
Hydrophobic interactions:
A:Y.152
,
A:N.209
,
A:Y.240
Water bridges:
A:Y.152
,
A:Y.240
,
A:S.269
Salt bridges:
A:R.278
pi-Stacking:
A:Y.152
PLP.5:
15 residues within 4Å:
Chain A:
Y.94
,
N.309
Chain B:
G.127
,
A.128
,
K.129
,
Y.152
,
C.205
,
N.209
,
D.237
,
Y.240
,
S.267
,
S.269
,
N.270
,
R.278
Ligands:
SO4.6
16
PLIP interactions
:
14 interactions with chain B
,
2 interactions with chain A
Hydrophobic interactions:
B:Y.152
,
B:N.209
Hydrogen bonds:
B:A.128
,
B:K.129
,
B:N.209
,
B:S.267
,
B:S.267
,
B:S.269
,
B:N.270
,
A:Y.94
,
A:N.309
Water bridges:
B:A.239
,
B:Y.240
,
B:S.269
Salt bridges:
B:R.278
pi-Stacking:
B:Y.152
5 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.2:
8 residues within 4Å:
Chain A:
F.39
,
I.63
,
G.64
,
Y.152
,
N.209
,
Y.240
,
R.404
Ligands:
PLP.1
6
PLIP interactions
:
6 interactions with chain A
Hydrogen bonds:
A:G.64
,
A:N.209
Water bridges:
A:Y.240
,
A:Y.240
,
A:N.270
Salt bridges:
A:R.404
SO4.3:
4 residues within 4Å:
Chain A:
K.101
,
R.104
,
D.119
,
D.120
2
PLIP interactions
:
2 interactions with chain A
Salt bridges:
A:K.101
,
A:R.104
SO4.6:
8 residues within 4Å:
Chain B:
F.39
,
I.63
,
G.64
,
Y.152
,
N.209
,
Y.240
,
R.404
Ligands:
PLP.5
7
PLIP interactions
:
6 interactions with chain B
,
1 interactions with chain A
Hydrogen bonds:
B:G.64
,
B:Y.152
,
B:N.209
,
B:N.209
Water bridges:
B:Y.240
,
A:Y.94
Salt bridges:
B:R.404
SO4.7:
4 residues within 4Å:
Chain B:
K.101
,
R.104
,
D.119
,
D.120
4
PLIP interactions
:
4 interactions with chain B
Water bridges:
B:K.101
,
B:K.101
Salt bridges:
B:K.101
,
B:R.104
SO4.8:
2 residues within 4Å:
Chain B:
G.176
,
N.177
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:N.177
Water bridges:
B:I.178
1 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.4:
6 residues within 4Å:
Chain A:
K.81
,
S.92
,
A.100
,
N.313
,
Q.316
,
A.317
6
PLIP interactions
:
6 interactions with chain A
Hydrogen bonds:
A:K.81
,
A:S.92
Water bridges:
A:S.92
,
A:N.313
,
A:Q.316
,
A:Q.316
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Watanabe, N. et al., Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana. J.Mol.Biol. (2008)
Release Date
2008-10-14
Peptides
LL-diaminopimelate aminotransferase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
Export Alignment
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Secondary Structure
None
DSSP
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Fade Mismatches
Enhance Mismatches
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2° Structure
Bfactor
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LL-diaminopimelate aminotransferase
Related Entries With Identical Sequence
3ei8.1
|
3ei9.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
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Outline
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Transparent
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