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SMTL ID : 4r5h.1
Crystal structure of sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide-Adenine-Dinucleotide-Phosphate and 3-carboxy-propenyl-phthalic acid
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.80 Å
Oligo State
homo-dimer
Ligands
8 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.1:
4 residues within 4Å:
Chain A:
E.24
,
S.25
,
W.332
,
E.339
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:E.24
Water bridges:
A:E.339
EDO.2:
7 residues within 4Å:
Chain A:
Q.17
,
S.250
,
V.297
,
G.298
,
D.324
,
L.326
,
L.327
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:S.250
,
A:G.298
EDO.3:
4 residues within 4Å:
Chain A:
L.311
,
D.312
Chain B:
T.225
,
K.229
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:K.229
,
B:D.235
Water bridges:
B:V.239
EDO.4:
6 residues within 4Å:
Chain A:
E.282
,
P.291
,
Q.292
,
N.295
,
A.296
,
F.303
5
PLIP interactions
:
5 interactions with chain A
Hydrogen bonds:
A:Q.292
,
A:Q.292
Water bridges:
A:N.295
,
A:N.295
,
A:N.295
EDO.9:
4 residues within 4Å:
Chain B:
E.24
,
S.25
,
W.332
,
E.339
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:E.24
Water bridges:
B:E.339
,
B:E.339
EDO.10:
6 residues within 4Å:
Chain B:
Q.17
,
S.250
,
G.298
,
D.324
,
L.326
,
L.327
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:S.250
,
B:G.298
Water bridges:
B:Q.17
EDO.11:
6 residues within 4Å:
Chain B:
E.282
,
P.291
,
Q.292
,
N.295
,
A.296
,
F.303
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:Q.292
,
B:Q.292
Water bridges:
B:N.295
,
B:N.295
EDO.12:
4 residues within 4Å:
Chain A:
T.225
,
K.229
Chain B:
L.311
,
D.312
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:K.229
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.5:
5 residues within 4Å:
Chain A:
I.273
,
A.274
,
A.275
,
F.276
,
A.279
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:A.274
,
A:A.279
NA.6:
1 residues within 4Å:
Chain A:
E.343
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:E.343
1 x
3JN
:
3-[(1E)-3-carboxyprop-1-en-1-yl]benzene-1,2-dicarboxylic acid
(Non-covalent)
3JN.7:
16 residues within 4Å:
Chain A:
S.74
,
N.94
,
T.95
,
S.96
,
R.99
,
N.127
,
C.128
,
Q.155
,
G.159
,
A.160
,
I.209
,
E.220
,
K.223
,
R.245
,
H.252
Ligands:
NAP.8
11
PLIP interactions
:
11 interactions with chain A
Hydrogen bonds:
A:S.74
,
A:S.96
,
A:N.127
,
A:Q.155
Water bridges:
A:S.74
,
A:S.74
Salt bridges:
A:R.99
,
A:K.223
,
A:K.223
,
A:R.245
,
A:H.252
2 x
NAP
:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
(Non-covalent)
NAP.8:
27 residues within 4Å:
Chain A:
G.9
,
A.10
,
T.11
,
G.12
,
A.13
,
V.14
,
A.36
,
S.37
,
R.39
,
S.40
,
T.57
,
S.71
,
A.72
,
G.73
,
T.76
,
N.94
,
T.95
,
C.125
,
P.126
,
N.127
,
C.128
,
S.158
,
G.161
,
M.162
,
G.329
,
A.330
Ligands:
3JN.7
25
PLIP interactions
:
25 interactions with chain A
Hydrophobic interactions:
A:V.14
Hydrogen bonds:
A:G.9
,
A:T.11
,
A:T.11
,
A:G.12
,
A:A.13
,
A:V.14
,
A:S.37
,
A:S.37
,
A:R.39
,
A:S.40
,
A:S.40
,
A:S.40
,
A:N.94
,
A:N.94
,
A:C.128
,
A:M.162
Water bridges:
A:G.15
,
A:A.72
,
A:S.74
,
A:S.74
,
A:Y.80
,
A:Y.80
,
A:G.163
Salt bridges:
A:R.39
NAP.13:
17 residues within 4Å:
Chain B:
G.9
,
A.10
,
T.11
,
G.12
,
A.13
,
A.36
,
S.37
,
R.39
,
S.40
,
T.57
,
S.71
,
A.72
,
T.76
,
A.160
,
G.161
,
M.162
,
G.163
20
PLIP interactions
:
20 interactions with chain B
Hydrogen bonds:
B:G.9
,
B:T.11
,
B:T.11
,
B:T.11
,
B:G.12
,
B:A.13
,
B:S.37
,
B:S.37
,
B:R.39
,
B:S.40
,
B:S.40
,
B:S.40
,
B:S.40
,
B:T.76
,
B:M.162
,
B:G.163
Water bridges:
B:V.14
,
B:V.14
,
B:T.57
,
B:Y.80
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Pavlovsky, A.G. et al., A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway. Acta Crystallogr.,Sect.D (2014)
Release Date
2014-12-10
Peptides
Aspartate-semialdehyde dehydrogenase:
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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2° Structure
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Aspartate-semialdehyde dehydrogenase
Related Entries With Identical Sequence
2gyy.1
|
2gyy.2
|
2gz1.1
|
2gz2.1
|
2gz3.1
|
2gz3.2
|
2gz3.3
|
3pwk.1
|
3pws.1
|
3pyl.1
|
3pyl.2
|
3pyx.1
|
3pzb.1
|
3q11.1
|
3q1l.1
|
3q1l.2
|
4r3n.1
|
4r3w.1
|
4r41.1
|
4r4j.1
|
4r51.1
|
4r54.1
Cartoon
Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog
Background
Transparent
Resolution
Low
Medium
High
Extreme