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SMTL ID : 1ini.1
CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.82 Å
Oligo State
homo-dimer
Ligands
2 x
MG
:
MAGNESIUM ION
(Non-covalent)
MG.1:
2 residues within 4Å:
Chain A:
R.20
Ligands:
CDM.2
No protein-ligand interaction detected (PLIP)
MG.3:
2 residues within 4Å:
Chain B:
R.20
Ligands:
CDM.4
No protein-ligand interaction detected (PLIP)
2 x
CDM
:
4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
(Non-covalent)
CDM.2:
25 residues within 4Å:
Chain A:
P.13
,
A.14
,
A.15
,
G.16
,
R.20
,
K.27
,
G.82
,
D.83
,
E.84
,
R.85
,
S.88
,
D.106
,
A.107
,
A.108
,
R.109
,
A.163
,
T.165
,
T.189
,
D.190
,
K.213
,
T.215
Chain B:
D.139
,
T.140
,
R.157
Ligands:
MG.1
19
PLIP interactions
:
15 interactions with chain A
,
4 interactions with chain B
Hydrophobic interactions:
A:T.165
,
A:D.190
Hydrogen bonds:
A:A.15
,
A:G.16
,
A:R.20
,
A:G.82
,
A:S.88
,
A:A.107
,
A:A.108
,
A:R.109
,
A:A.163
,
B:D.139
,
B:T.140
,
B:R.157
Salt bridges:
A:R.20
,
A:K.27
,
A:K.213
,
A:K.213
,
B:R.157
CDM.4:
25 residues within 4Å:
Chain A:
D.139
,
T.140
,
R.157
Chain B:
P.13
,
A.14
,
A.15
,
G.16
,
R.20
,
K.27
,
G.82
,
D.83
,
E.84
,
R.85
,
S.88
,
D.106
,
A.107
,
A.108
,
R.109
,
A.163
,
T.165
,
T.189
,
D.190
,
K.213
,
T.215
Ligands:
MG.3
19
PLIP interactions
:
15 interactions with chain B
,
4 interactions with chain A
Hydrophobic interactions:
B:T.165
,
B:D.190
Hydrogen bonds:
B:A.15
,
B:G.16
,
B:R.20
,
B:G.82
,
B:S.88
,
B:A.107
,
B:A.108
,
B:R.109
,
B:A.163
,
A:T.140
,
A:T.140
,
A:R.157
Salt bridges:
B:R.20
,
B:K.27
,
B:K.213
,
B:K.213
,
A:R.157
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Richard, S.B. et al., Structure of 4-diphosphocytidyl-2-C- methylerythritol synthetase involved in mevalonate- independent isoprenoid biosynthesis. Nat.Struct.Biol. (2001)
Release Date
2001-11-14
Peptides
4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
A
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4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE
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