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3ZE3
Biol. Unit 2
Info
Asym.Unit (214 KB)
Biol.Unit 1 (98 KB)
Biol.Unit 2 (108 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE - DELTA7
Authors
:
D. Li, V. E. Pye, J. A. Lyons, L. Vogeley, D. Aragao, M. Caffrey
Date
:
03 Dec 12 (Deposition) - 22 May 13 (Release) - 05 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: D,E,F (1x)
Biol. Unit 2: A,B,C (1x)
Keywords
:
Transferase, Lipid Metabolism, In Meso Crystallisation, Lipid Cubic Phase, Lipidic Mesophase, Thermostable Mutant, Monoacylglycerol, 7. 8 Mag
(Keyword Search:
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Reference
:
D. Li, J. A. Lyons, V. E. Pye, L. Vogeley, D. Aragao, C. P. Kenyon, S. T. A. Shah, C. Doherty, M. Aherne, M. Caffrey
Crystal Structure Of The Integral Membrane Diacylglycerol Kinase.
Nature V. 497 521 2013
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Hetero Components
(2, 9)
Info
All Hetero Components
1a: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Ma)
1b: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Mb)
1c: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Mc)
1d: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Md)
1e: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Me)
1f: (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Mf)
2a: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Na)
2b: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nb)
2c: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nc)
2d: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nd)
2e: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Ne)
2f: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Nf)
2g: (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTA... (78Ng)
3a: ACETATE ION (ACTa)
4a: CITRATE ANION (FLCa)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
6a: ZINC ION (ZNa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
78M
2
Ligand/Ion
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
2
78N
7
Ligand/Ion
(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3
ACT
-1
Ligand/Ion
ACETATE ION
4
FLC
-1
Ligand/Ion
CITRATE ANION
5
NA
-1
Ligand/Ion
SODIUM ION
6
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(13, 13)
Info
All Sites
01: AC6 (SOFTWARE)
02: AC7 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: BC9 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
01
AC6
SOFTWARE
ALA A:13 , ALA A:14 , SER A:17 , 78N A:1123 , 78N A:1124 , SER B:98 , VAL B:101 , LEU B:102 , ILE B:105 , ILE B:110 , 78N B:1123
BINDING SITE FOR RESIDUE 78N B1122
02
AC7
SOFTWARE
ARG A:9 , 78N A:1124 , GLU B:34 , VAL B:65 , GLU B:69 , ALA B:108 , TRP B:112 , ALA B:113 , 78N B:1122
BINDING SITE FOR RESIDUE 78N B1123
03
AC8
SOFTWARE
GLN A:33 , GLU A:34 , 78M A:1126 , TRP C:117 , 78N C:1122 , TRP D:25 , ALA D:29 , ARG D:32 , GLN D:33 , VAL D:36 , HOH D:2017 , HOH D:2049
BINDING SITE FOR RESIDUE 78M D1125
04
AC9
SOFTWARE
78M A:1126 , ALA B:46 , ARG B:55 , HOH B:2010 , ILE C:110 , ILE C:114 , TRP C:117 , SER C:118 , GLN D:33 , 78M D:1125
BINDING SITE FOR RESIDUE 78N C1122
05
BC1
SOFTWARE
TRP A:18 , ARG A:22 , TRP A:25 , ILE A:26 , LEU A:39 , MET A:63 , MET A:66
BINDING SITE FOR RESIDUE 78N A1122
06
BC2
SOFTWARE
ALA A:30 , PHE A:31 , GLU A:34 , GLU A:69 , LEU A:102 , ILE A:105 , HOH A:2012 , ARG D:22 , TRP D:25 , HOH D:2050
BINDING SITE FOR RESIDUE 78M D1126
07
BC3
SOFTWARE
TRP B:47 , HOH B:2006 , HOH B:2008 , LEU D:102 , VAL D:109 , ALA D:113 , HOH D:2018 , HOH D:2043
BINDING SITE FOR RESIDUE 78M D1127
08
BC4
SOFTWARE
LEU A:40 , TRP A:47 , 78M A:1126 , GLU C:34 , GLU C:69 , TRP C:112
BINDING SITE FOR RESIDUE 78N C1123
09
BC5
SOFTWARE
TRP A:117 , GLY B:35 , VAL B:36 , TRP D:47 , LEU D:48 , ASP D:49 , PHE D:120
BINDING SITE FOR RESIDUE 78M D1128
10
BC6
SOFTWARE
VAL A:42 , ALA A:46 , ARG A:55 , 78N A:1124 , HOH A:2016 , 78N B:1122
BINDING SITE FOR RESIDUE 78N A1123
11
BC7
SOFTWARE
VAL A:50 , ASP A:51 , ALA A:52 , ARG A:55 , 78N A:1123 , ILE B:114 , TRP B:117 , 78N B:1122 , 78N B:1123
BINDING SITE FOR RESIDUE 78N A1124
12
BC8
SOFTWARE
ILE A:110 , TRP A:117 , ALA D:46 , TRP D:47 , ARG D:55
BINDING SITE FOR RESIDUE 78M A1125
13
BC9
SOFTWARE
CYS A:41 , PHE A:120 , HOH A:2015 , LEU C:102 , ILE C:105 , 78N C:1122 , 78N C:1123 , LEU D:39 , 78M D:1125
BINDING SITE FOR RESIDUE 78M A1126
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: DAGK_PROKAR (A:69-80,B:69-80,C:69-80)
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DAGK_PROKAR
PS01069
Prokaryotic diacylglycerol kinase signature.
KDGL_ECOLI
70-81
3
A:69-80
B:69-80
C:69-80
-
-
-
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
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Asymmetric Unit 1
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Asym.Unit (214 KB)
Header - Asym.Unit
Biol.Unit 1 (98 KB)
Header - Biol.Unit 1
Biol.Unit 2 (108 KB)
Header - Biol.Unit 2
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