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2R4J
Biol. Unit 1
Info
Asym.Unit (187 KB)
Biol.Unit 1 (92 KB)
Biol.Unit 2 (92 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ESCHERICHIA COLI SEMET SUBSTITUTED GLYCEROL-3-PHOSPHATE DEHYDROGENASE IN COMPLEX WITH DHAP
Authors
:
J. I. Yeh, S. Du, U. Chinte
Date
:
31 Aug 07 (Deposition) - 03 Jun 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.96
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Glpd, Cytoplasm, Fad, Flavoprotein, Glycerol Metabolism, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. I. Yeh, U. Chinte, S. Du
Structure Of Glycerol-3-Phosphate Dehydrogenase, An Essential Monotopic Membrane Enzyme Involved In Respiration And Metabolism.
Proc. Natl. Acad. Sci. Usa V. 105 3280 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(8, 31)
Info
All Hetero Components
1a: 1,3-DIHYDROXYACETONEPHOSPHATE (13Pa)
1b: 1,3-DIHYDROXYACETONEPHOSPHATE (13Pb)
2a: BICINE (BCNa)
2b: BICINE (BCNb)
2c: BICINE (BCNc)
3a: B-OCTYLGLUCOSIDE (BOGa)
3b: B-OCTYLGLUCOSIDE (BOGb)
3c: B-OCTYLGLUCOSIDE (BOGc)
3d: B-OCTYLGLUCOSIDE (BOGd)
3e: B-OCTYLGLUCOSIDE (BOGe)
3f: B-OCTYLGLUCOSIDE (BOGf)
4a: 1,2-ETHANEDIOL (EDOa)
4b: 1,2-ETHANEDIOL (EDOb)
4c: 1,2-ETHANEDIOL (EDOc)
4d: 1,2-ETHANEDIOL (EDOd)
4e: 1,2-ETHANEDIOL (EDOe)
4f: 1,2-ETHANEDIOL (EDOf)
4g: 1,2-ETHANEDIOL (EDOg)
4h: 1,2-ETHANEDIOL (EDOh)
4i: 1,2-ETHANEDIOL (EDOi)
4j: 1,2-ETHANEDIOL (EDOj)
4k: 1,2-ETHANEDIOL (EDOk)
4l: 1,2-ETHANEDIOL (EDOl)
4m: 1,2-ETHANEDIOL (EDOm)
4n: 1,2-ETHANEDIOL (EDOn)
4o: 1,2-ETHANEDIOL (EDOo)
4p: 1,2-ETHANEDIOL (EDOp)
4q: 1,2-ETHANEDIOL (EDOq)
4r: 1,2-ETHANEDIOL (EDOr)
4s: 1,2-ETHANEDIOL (EDOs)
4t: 1,2-ETHANEDIOL (EDOt)
4u: 1,2-ETHANEDIOL (EDOu)
4v: 1,2-ETHANEDIOL (EDOv)
4w: 1,2-ETHANEDIOL (EDOw)
4x: 1,2-ETHANEDIOL (EDOx)
4y: 1,2-ETHANEDIOL (EDOy)
4z: 1,2-ETHANEDIOL (EDOz)
5a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
5b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
6a: IMIDAZOLE (IMDa)
6b: IMIDAZOLE (IMDb)
6c: IMIDAZOLE (IMDc)
6d: IMIDAZOLE (IMDd)
6e: IMIDAZOLE (IMDe)
6f: IMIDAZOLE (IMDf)
7a: SELENOMETHIONINE (MSEa)
7b: SELENOMETHIONINE (MSEb)
7c: SELENOMETHIONINE (MSEc)
7d: SELENOMETHIONINE (MSEd)
7e: SELENOMETHIONINE (MSEe)
7f: SELENOMETHIONINE (MSEf)
7g: SELENOMETHIONINE (MSEg)
7h: SELENOMETHIONINE (MSEh)
7i: SELENOMETHIONINE (MSEi)
7j: SELENOMETHIONINE (MSEj)
7k: SELENOMETHIONINE (MSEk)
7l: SELENOMETHIONINE (MSEl)
7m: SELENOMETHIONINE (MSEm)
7n: SELENOMETHIONINE (MSEn)
8a: PHOSPHATE ION (PO4a)
8b: PHOSPHATE ION (PO4b)
9a: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
13P
1
Ligand/Ion
1,3-DIHYDROXYACETONEPHOSPHATE
2
BCN
1
Ligand/Ion
BICINE
3
BOG
4
Ligand/Ion
B-OCTYLGLUCOSIDE
4
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
5
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
6
IMD
5
Ligand/Ion
IMIDAZOLE
7
MSE
7
Mod. Amino Acid
SELENOMETHIONINE
8
PO4
1
Ligand/Ion
PHOSPHATE ION
9
TAM
-1
Ligand/Ion
TRIS(HYDROXYETHYL)AMINOMETHANE
[
close Hetero Component info
]
Sites
(29, 29)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC7 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC2 (SOFTWARE)
11: CC3 (SOFTWARE)
12: CC4 (SOFTWARE)
13: CC6 (SOFTWARE)
14: CC9 (SOFTWARE)
15: DC1 (SOFTWARE)
16: DC2 (SOFTWARE)
17: DC3 (SOFTWARE)
18: DC4 (SOFTWARE)
19: DC6 (SOFTWARE)
20: DC8 (SOFTWARE)
21: DC9 (SOFTWARE)
22: EC1 (SOFTWARE)
23: EC2 (SOFTWARE)
24: EC4 (SOFTWARE)
25: EC5 (SOFTWARE)
26: EC7 (SOFTWARE)
27: FC1 (SOFTWARE)
28: FC2 (SOFTWARE)
29: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:99 , ARG A:102 , ARG A:137 , BOG A:1949 , BOG A:1950 , TYR B:59
BINDING SITE FOR RESIDUE BOG A 700
02
AC2
SOFTWARE
LEU A:53 , ARG A:54 , LEU A:56 , GLU A:57 , TYR A:59 , PHE A:61 , LEU A:89 , ARG A:96 , GLN A:249
BINDING SITE FOR RESIDUE BOG A 800
03
AC5
SOFTWARE
TRP A:99 , BOG A:700
BINDING SITE FOR RESIDUE BOG A 1949
04
AC6
SOFTWARE
HIS A:91 , PRO A:93 , ALA A:98 , ARG A:137 , BOG A:700
BINDING SITE FOR RESIDUE BOG A 1950
05
AC7
SOFTWARE
ARG A:161 , TYR B:398 , ARG B:401 , ARG B:405 , HOH B:894
BINDING SITE FOR RESIDUE PO4 B 801
06
AC8
SOFTWARE
ILE A:183 , SER A:196 , TRP A:197 , GLN A:198
BINDING SITE FOR RESIDUE PO4 A 1951
07
AC9
SOFTWARE
ILE A:9 , GLY A:12 , ILE A:13 , ASN A:14 , LEU A:32 , GLU A:33 , ALA A:34 , CYS A:39 , THR A:41 , SER A:42 , ALA A:44 , SER A:45 , SER A:46 , LYS A:47 , LEU A:48 , ALA A:172 , THR A:206 , GLY A:207 , GLY A:231 , THR A:270 , ARG A:317 , GLY A:353 , LYS A:354 , LEU A:355 , THR A:356 , EDO A:1952 , HOH A:1972 , HOH A:1986 , HOH A:1988 , HOH A:2075 , HOH A:2076
BINDING SITE FOR RESIDUE FAD A 600
08
BC7
SOFTWARE
ALA A:34 , FAD A:600
BINDING SITE FOR RESIDUE EDO A 1952
09
CC1
SOFTWARE
SER A:43 , TRP A:468 , ARG A:469 , EDO A:1954 , EDO A:1965
BINDING SITE FOR RESIDUE EDO A 1953
10
CC2
SOFTWARE
TRP A:311 , EDO A:1953
BINDING SITE FOR RESIDUE EDO A 1954
11
CC3
SOFTWARE
ASN A:294 , THR A:298 , EDO B:817
BINDING SITE FOR RESIDUE EDO A 1955
12
CC4
SOFTWARE
ASN A:290 , LEU A:293 , ASN A:294 , ASN B:294 , HOH B:822 , HOH B:856
BINDING SITE FOR RESIDUE EDO A 1956
13
CC6
SOFTWARE
MSE A:262 , HIS A:416 , LYS A:472 , GLN A:473 , TRP A:476 , IMD A:1960 , HOH A:1995
BINDING SITE FOR RESIDUE EDO A 1957
14
CC9
SOFTWARE
THR A:41 , PRO A:279 , LYS A:280 , GLY A:315 , VAL A:316 , HOH A:2097
BINDING SITE FOR RESIDUE EDO A 1958
15
DC1
SOFTWARE
HIS A:457 , IMD A:1961 , IMD A:1963 , ARG B:405
BINDING SITE FOR RESIDUE EDO A 1959
16
DC2
SOFTWARE
HIS A:416 , HIS A:444 , GLU A:445 , GLN A:473 , EDO A:1957
BINDING SITE FOR RESIDUE IMD A 1960
17
DC3
SOFTWARE
ARG A:405 , GLN B:157 , VAL B:160 , ARG B:161 , HIS B:457 , EDO B:811
BINDING SITE FOR RESIDUE TAM B 812
18
DC4
SOFTWARE
ASN A:424 , LEU A:427 , EDO A:1959 , HOH A:2058
BINDING SITE FOR RESIDUE IMD A 1961
19
DC6
SOFTWARE
ARG A:405 , ARG B:161
BINDING SITE FOR RESIDUE EDO A 1962
20
DC8
SOFTWARE
VAL A:455 , ASP A:456 , HIS A:457 , GLU A:458 , TRP A:459 , EDO A:1959
BINDING SITE FOR RESIDUE IMD A 1963
21
DC9
SOFTWARE
PHE A:106
BINDING SITE FOR RESIDUE EDO A 1964
22
EC1
SOFTWARE
CYS A:39 , ALA A:40 , SER A:43 , ALA A:44 , TYR A:313 , SER A:314 , EDO A:1953 , HOH A:2092 , HOH A:2097
BINDING SITE FOR RESIDUE EDO A 1965
23
EC2
SOFTWARE
PRO A:237 , VAL A:310
BINDING SITE FOR RESIDUE IMD A 1966
24
EC4
SOFTWARE
PRO A:208 , LEU A:228 , PRO A:279 , HOH A:2002
BINDING SITE FOR RESIDUE IMD A 1967
25
EC5
SOFTWARE
ARG A:54 , TYR A:55 , ARG A:254 , ILE A:255 , THR A:270 , ASP A:272 , ARG A:317 , ARG A:332 , HOH A:2100
BINDING SITE FOR RESIDUE 13P A 1968
26
EC7
SOFTWARE
EDO A:1955 , GLN B:303 , EDO B:803
BINDING SITE FOR RESIDUE EDO B 817
27
FC1
SOFTWARE
GLU A:274 , GLU A:285 , SER A:287 , ASP B:272 , VAL B:273 , GLU B:274 , BCN B:821
BINDING SITE FOR RESIDUE BCN B 820
28
FC2
SOFTWARE
ASP A:272 , VAL A:273 , SER A:287 , GLU B:285 , SER B:287 , BCN B:820 , HOH B:910
BINDING SITE FOR RESIDUE BCN B 821
29
FC3
SOFTWARE
GLY A:26 , LYS A:162 , ARG B:404
BINDING SITE FOR RESIDUE BCN A 1969
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: FAD_G3PDH_1 (A:9-26)
2: FAD_G3PDH_2 (A:352-362)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FAD_G3PDH_1
PS00977
FAD-dependent glycerol-3-phosphate dehydrogenase signature 1.
GLPD_ECOLI
9-26
1
A:9-26
-
2
FAD_G3PDH_2
PS00978
FAD-dependent glycerol-3-phosphate dehydrogenase signature 2.
GLPD_ECOLI
352-362
1
A:352-362
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_DAO_2r4jB01 (B:5-359)
1b: PFAM_DAO_2r4jB02 (B:5-359)
View:
Select:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
DAO
(25)
Escherichia coli (strain K12)
(6)
1a
DAO-2r4jB01
B:5-359
1b
DAO-2r4jB02
B:5-359
[
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]
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Asymmetric Unit 1
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