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SMTL ID : 4hgd.2
(1 other biounit)
Structural insights into yeast Nit2: C169S mutant of yeast Nit2 in complex with an endogenous peptide-like ligand
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.04 Å
Oligo State
homo-dimer
Ligands
5 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.1:
4 residues within 4Å:
Chain A:
Y.93
,
K.97
,
D.266
,
E.268
6
PLIP interactions
:
6 interactions with chain A
Hydrogen bonds:
A:K.97
,
A:D.266
,
A:W.269
Water bridges:
A:Y.93
,
A:K.97
,
A:E.268
GOL.2:
3 residues within 4Å:
Chain A:
L.156
,
Q.157
,
D.189
No protein-ligand interaction detected (PLIP)
GOL.5:
6 residues within 4Å:
Chain A:
A.236
,
H.237
Chain B:
R.243
,
W.296
,
G.297
,
K.298
5
PLIP interactions
:
5 interactions with chain B
Hydrogen bonds:
B:R.243
,
B:W.296
,
B:W.296
Water bridges:
B:G.297
,
B:I.299
GOL.6:
3 residues within 4Å:
Chain B:
S.107
,
T.110
Ligands:
GOL.7
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:T.110
GOL.7:
6 residues within 4Å:
Chain B:
Q.106
,
S.107
,
E.152
,
G.153
,
K.154
Ligands:
GOL.6
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:S.107
2 x
CAC
:
CACODYLATE ION
(Non-covalent)
CAC.3:
3 residues within 4Å:
Chain A:
I.102
,
L.128
,
E.158
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:E.158
CAC.8:
2 residues within 4Å:
Chain B:
C.48
,
M.261
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:M.261
2 x
KGT
:
N-(4-carboxy-4-oxobutanoyl)-L-cysteinylglycine
(Non-covalent)
KGT.4:
15 residues within 4Å:
Chain A:
E.79
,
L.84
,
H.127
,
N.144
,
K.161
,
F.165
,
E.177
,
S.203
,
Y.204
,
R.207
,
A.228
,
F.229
,
T.230
,
T.233
,
R.284
15
PLIP interactions
:
15 interactions with chain A
Hydrophobic interactions:
A:F.165
Hydrogen bonds:
A:N.144
,
A:K.161
,
A:E.177
,
A:S.203
,
A:Y.204
,
A:A.228
,
A:T.230
,
A:T.233
,
A:R.284
,
A:R.284
Water bridges:
A:S.180
Salt bridges:
A:H.127
,
A:R.207
,
A:R.284
KGT.9:
15 residues within 4Å:
Chain B:
E.79
,
L.84
,
H.127
,
N.144
,
K.161
,
F.165
,
E.177
,
S.203
,
Y.204
,
R.207
,
A.228
,
F.229
,
T.230
,
T.233
,
R.284
17
PLIP interactions
:
17 interactions with chain B
Hydrophobic interactions:
B:F.165
,
B:Y.204
,
B:F.229
,
B:F.229
Hydrogen bonds:
B:N.144
,
B:K.161
,
B:E.177
,
B:S.203
,
B:Y.204
,
B:A.228
,
B:T.230
,
B:T.233
,
B:R.284
,
B:R.284
Salt bridges:
B:H.127
,
B:R.207
,
B:R.284
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Liu, H. et al., Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2. Acta Crystallogr.,Sect.D (2013)
Release Date
2013-07-31
Peptides
Probable hydrolase NIT2:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
B
B
C
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Probable hydrolase NIT2
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Rope
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