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SMTL ID : 1kc1.1
Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 2.60 Å
Oligo State
homo-dimer
Ligands
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
4 residues within 4Å:
Chain A:
E.190
Chain B:
E.15
,
E.190
Ligands:
MG.4
No protein-ligand interaction detected (PLIP)
MG.4:
4 residues within 4Å:
Chain A:
E.15
,
E.190
Chain B:
E.190
Ligands:
MG.1
No protein-ligand interaction detected (PLIP)
2 x
SO4
:
SULFATE ION
(Non-functional Binders)
SO4.2:
2 residues within 4Å:
Chain A:
K.158
Chain B:
T.295
1
PLIP interactions
:
1 interactions with chain A
Salt bridges:
A:K.158
SO4.5:
2 residues within 4Å:
Chain A:
T.295
Chain B:
K.158
1
PLIP interactions
:
1 interactions with chain B
Salt bridges:
B:K.158
2 x
NDP
:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
(Non-covalent)
NDP.3:
20 residues within 4Å:
Chain A:
T.9
,
G.10
,
Q.11
,
V.12
,
V.31
,
G.38
,
D.39
,
F.40
,
A.61
,
A.62
,
A.63
,
T.65
,
L.80
,
Y.102
,
S.103
,
T.104
,
Y.128
,
K.132
,
T.151
,
V.154
18
PLIP interactions
:
18 interactions with chain A
Hydrophobic interactions:
A:V.154
Hydrogen bonds:
A:Q.11
,
A:Q.11
,
A:V.12
,
A:D.39
,
A:D.39
,
A:F.40
,
A:A.63
,
A:Y.128
,
A:K.132
,
A:V.154
Water bridges:
A:G.7
,
A:G.10
,
A:G.13
,
A:V.31
,
A:H.101
,
A:Y.102
,
A:W.153
NDP.6:
20 residues within 4Å:
Chain B:
T.9
,
G.10
,
Q.11
,
V.12
,
V.31
,
G.38
,
D.39
,
F.40
,
A.61
,
A.62
,
A.63
,
T.65
,
L.80
,
Y.102
,
S.103
,
T.104
,
Y.128
,
K.132
,
T.151
,
V.154
18
PLIP interactions
:
18 interactions with chain B
Hydrophobic interactions:
B:V.154
Hydrogen bonds:
B:Q.11
,
B:Q.11
,
B:V.12
,
B:D.39
,
B:D.39
,
B:F.40
,
B:A.63
,
B:Y.128
,
B:K.132
,
B:V.154
Water bridges:
B:G.7
,
B:G.10
,
B:G.13
,
B:V.31
,
B:H.101
,
B:Y.102
,
B:W.153
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Blankenfeldt, W. et al., Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode. Structure (2002)
Release Date
2002-06-28
Peptides
dTDP-glucose oxidoreductase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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dTDP-glucose oxidoreductase
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