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SMTL ID : 2r0t.1
Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.90 Å
Oligo State
homo-dimer
Ligands
2 x
PGU
:
N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid
(Covalent)
PGU.1:
21 residues within 4Å:
Chain A:
S.57
,
G.58
,
S.59
,
N.62
,
S.89
,
W.90
,
T.92
,
T.93
,
V.135
,
D.161
,
C.163
,
E.164
,
S.185
,
F.187
,
K.190
,
G.197
,
R.333
Chain B:
H.217
,
W.219
,
N.250
,
R.252
20
PLIP interactions
:
15 interactions with chain A
,
5 interactions with chain B
Hydrophobic interactions:
A:W.90
,
A:V.135
,
A:F.187
Hydrogen bonds:
A:S.57
,
A:G.58
,
A:S.59
,
A:N.62
,
A:T.93
,
A:E.164
,
A:E.164
,
A:S.185
,
A:S.185
,
B:N.250
Salt bridges:
A:K.190
,
A:K.190
,
A:R.333
,
B:H.217
,
B:H.217
,
B:R.252
Water bridges:
B:R.221
PGU.2:
20 residues within 4Å:
Chain A:
H.217
,
W.219
,
N.250
,
R.252
Chain B:
S.57
,
G.58
,
S.59
,
N.62
,
S.89
,
W.90
,
T.92
,
T.93
,
D.161
,
C.163
,
E.164
,
S.185
,
F.187
,
K.190
,
G.197
,
R.333
17
PLIP interactions
:
13 interactions with chain B
,
4 interactions with chain A
Hydrophobic interactions:
B:W.90
,
B:W.90
,
B:W.90
,
B:F.187
Hydrogen bonds:
B:S.57
,
B:G.58
,
B:S.59
,
B:N.62
,
B:T.93
,
B:E.164
,
B:S.185
,
A:N.250
Salt bridges:
B:K.190
,
B:R.333
,
A:H.217
,
A:H.217
,
A:R.252
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Cook, P.D. et al., A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation. Biochemistry (2007)
Release Date
2007-12-18
Peptides
Pyridoxamine 5-phosphate-dependent dehydrase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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