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SMTL ID : 2oga.1
(2 other biounits)
X-ray crystal structure of S. venezuelae DesV in complex with ketimine intermediate
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.05 Å
Oligo State
homo-dimer
Ligands
2 x
CL
:
CHLORIDE ION
(Non-functional Binders)
CL.1:
3 residues within 4Å:
Chain A:
Y.59
,
L.60
Chain B:
L.35
Ligand excluded by PLIP
CL.6:
2 residues within 4Å:
Chain B:
Y.59
,
L.60
Ligand excluded by PLIP
1 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.2:
2 residues within 4Å:
Chain A:
N.85
Chain B:
N.85
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:N.85
Water bridges:
B:D.259
4 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.3:
5 residues within 4Å:
Chain A:
A.74
,
Y.75
,
E.77
,
R.192
,
R.197
5
PLIP interactions
:
5 interactions with chain A
Hydrogen bonds:
A:Y.75
,
A:E.77
,
A:R.192
,
A:R.192
,
A:R.197
EDO.4:
8 residues within 4Å:
Chain A:
L.33
,
P.211
,
K.213
,
N.214
,
G.216
,
R.269
,
R.280
,
P.375
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:G.216
,
A:R.280
Water bridges:
A:N.214
,
A:G.216
EDO.7:
8 residues within 4Å:
Chain B:
L.33
,
L.35
,
P.211
,
K.213
,
N.214
,
G.216
,
R.269
,
P.375
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:G.216
,
B:R.269
Water bridges:
B:R.280
,
B:R.280
EDO.8:
4 residues within 4Å:
Chain B:
R.192
,
R.197
,
D.274
,
D.307
6
PLIP interactions
:
6 interactions with chain B
Hydrogen bonds:
B:R.192
,
B:R.197
,
B:R.197
,
B:D.274
Water bridges:
B:D.307
,
B:D.307
2 x
PGU
:
N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid
(Non-covalent)
PGU.5:
17 residues within 4Å:
Chain A:
S.86
,
G.87
,
M.88
,
Y.113
,
A.115
,
D.184
,
A.186
,
Q.187
,
S.208
,
Y.210
,
K.213
,
G.221
,
Y.338
Chain B:
Y.241
,
Y.247
,
N.255
,
R.257
20
PLIP interactions
:
4 interactions with chain B
,
16 interactions with chain A
Hydrogen bonds:
B:Y.241
,
B:Y.247
,
B:N.255
,
A:G.87
,
A:M.88
,
A:Q.187
,
A:S.208
,
A:S.208
,
A:K.213
,
A:Y.338
,
A:Y.338
Salt bridges:
B:R.257
,
A:K.213
Hydrophobic interactions:
A:Y.113
,
A:Y.113
,
A:A.115
,
A:A.186
,
A:Q.187
,
A:Y.210
Water bridges:
A:Y.210
PGU.9:
19 residues within 4Å:
Chain A:
Y.241
,
K.246
,
Y.247
,
N.255
,
R.257
Chain B:
S.86
,
G.87
,
M.88
,
Y.113
,
A.115
,
V.158
,
D.184
,
A.186
,
Q.187
,
S.208
,
Y.210
,
K.213
,
G.221
,
Y.338
23
PLIP interactions
:
18 interactions with chain B
,
5 interactions with chain A
Hydrophobic interactions:
B:Y.113
,
B:Y.113
,
B:A.115
,
B:V.158
,
B:A.186
,
B:Q.187
Hydrogen bonds:
B:G.87
,
B:M.88
,
B:Q.187
,
B:S.208
,
B:S.208
,
B:K.213
,
B:Y.338
,
B:Y.338
,
A:Y.241
,
A:N.255
Water bridges:
B:Y.113
,
B:A.186
,
B:Y.210
Salt bridges:
B:K.213
,
A:K.246
,
A:K.246
,
A:R.257
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Burgie, E.S. et al., Molecular architecture of DesV from Streptomyces venezuelae: A PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine. Protein Sci. (2007)
Release Date
2007-05-15
Peptides
Transaminase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Related Entries With Identical Sequence
2oga.2
|
2oga.3
|
2oge.1
|
2oge.2
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