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2R4J
Asym. Unit
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
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Hetero Components
(9, 62)
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
2
Ligand/Ion
1,3-DIHYDROXYACETONEPHOSPHATE
2
BCN
3
Ligand/Ion
BICINE
3
BOG
6
Ligand/Ion
B-OCTYLGLUCOSIDE
4
EDO
26
Ligand/Ion
1,2-ETHANEDIOL
5
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
6
IMD
6
Ligand/Ion
IMIDAZOLE
7
MSE
14
Mod. Amino Acid
SELENOMETHIONINE
8
PO4
2
Ligand/Ion
PHOSPHATE ION
9
TAM
1
Ligand/Ion
TRIS(HYDROXYETHYL)AMINOMETHANE
[
close Hetero Component info
]
Sites
(48, 48)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: 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
AC3
SOFTWARE
TRP B:99 , ARG B:102 , ILE B:103 , ARG B:137
BINDING SITE FOR RESIDUE BOG B 700
04
AC4
SOFTWARE
LEU B:53 , ARG B:54 , LEU B:56 , GLU B:57 , TYR B:59 , PHE B:61 , ARG B:96 , MET B:100 , ILE B:101 , GLY B:104 , LEU B:105 , ILE B:255
BINDING SITE FOR RESIDUE BOG B 800
05
AC5
SOFTWARE
TRP A:99 , BOG A:700
BINDING SITE FOR RESIDUE BOG A 1949
06
AC6
SOFTWARE
HIS A:91 , PRO A:93 , ALA A:98 , ARG A:137 , BOG A:700
BINDING SITE FOR RESIDUE BOG A 1950
07
AC7
SOFTWARE
ARG A:161 , TYR B:398 , ARG B:401 , ARG B:405 , HOH B:894
BINDING SITE FOR RESIDUE PO4 B 801
08
AC8
SOFTWARE
ILE A:183 , SER A:196 , TRP A:197 , GLN A:198
BINDING SITE FOR RESIDUE PO4 A 1951
09
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
10
BC1
SOFTWARE
ILE B:9 , GLY B:10 , GLY B:12 , ILE B:13 , ASN B:14 , GLU B:33 , ALA B:34 , CYS B:39 , ALA B:40 , THR B:41 , SER B:42 , ALA B:44 , SER B:45 , SER B:46 , LYS B:47 , LEU B:48 , ALA B:172 , THR B:206 , GLY B:207 , PRO B:208 , TRP B:209 , GLY B:231 , THR B:270 , ARG B:317 , GLY B:353 , LYS B:354 , LEU B:355 , THR B:356 , EDO B:804 , HOH B:827 , HOH B:831 , HOH B:924 , HOH B:948
BINDING SITE FOR RESIDUE FAD B 600
11
BC2
SOFTWARE
ARG B:254 , THR B:271 , ASP B:272 , HOH B:909 , HOH B:919
BINDING SITE FOR RESIDUE EDO B 802
12
BC3
SOFTWARE
LEU B:293 , ASN B:294 , ASN B:297 , EDO B:817 , HOH B:822
BINDING SITE FOR RESIDUE EDO B 803
13
BC4
SOFTWARE
ALA B:34 , ARG B:171 , FAD B:600 , HOH B:924 , HOH B:937
BINDING SITE FOR RESIDUE EDO B 804
14
BC5
SOFTWARE
TRP B:311 , TRP B:468
BINDING SITE FOR RESIDUE EDO B 805
15
BC6
SOFTWARE
SER B:43 , TRP B:468 , ARG B:469 , HOH B:843 , HOH B:958
BINDING SITE FOR RESIDUE EDO B 806
16
BC7
SOFTWARE
ALA A:34 , FAD A:600
BINDING SITE FOR RESIDUE EDO A 1952
17
BC8
SOFTWARE
MSE B:262 , HIS B:416 , LYS B:472 , GLN B:473 , EDO B:808 , HOH B:853
BINDING SITE FOR RESIDUE EDO B 807
18
BC9
SOFTWARE
HIS B:444 , GLU B:445 , GLN B:473 , EDO B:807
BINDING SITE FOR RESIDUE EDO B 808
19
CC1
SOFTWARE
SER A:43 , TRP A:468 , ARG A:469 , EDO A:1954 , EDO A:1965
BINDING SITE FOR RESIDUE EDO A 1953
20
CC2
SOFTWARE
TRP A:311 , EDO A:1953
BINDING SITE FOR RESIDUE EDO A 1954
21
CC3
SOFTWARE
ASN A:294 , THR A:298 , EDO B:817
BINDING SITE FOR RESIDUE EDO A 1955
22
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
23
CC5
SOFTWARE
ILE B:289 , ARG B:306
BINDING SITE FOR RESIDUE EDO B 809
24
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
25
CC7
SOFTWARE
PRO B:208 , GLN B:212 , LEU B:228 , PRO B:279 , HOH B:838
BINDING SITE FOR RESIDUE EDO B 810
26
CC8
SOFTWARE
VAL B:455 , ASP B:456 , HIS B:457 , GLU B:458 , TRP B:459 , TAM B:812
BINDING SITE FOR RESIDUE EDO B 811
27
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
28
DC1
SOFTWARE
HIS A:457 , IMD A:1961 , IMD A:1963 , ARG B:405
BINDING SITE FOR RESIDUE EDO A 1959
29
DC2
SOFTWARE
HIS A:416 , HIS A:444 , GLU A:445 , GLN A:473 , EDO A:1957
BINDING SITE FOR RESIDUE IMD A 1960
30
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
31
DC4
SOFTWARE
ASN A:424 , LEU A:427 , EDO A:1959 , HOH A:2058
BINDING SITE FOR RESIDUE IMD A 1961
32
DC5
SOFTWARE
ALA B:40 , THR B:41 , PRO B:279 , LYS B:280 , GLY B:315 , VAL B:316 , HOH B:869
BINDING SITE FOR RESIDUE EDO B 813
33
DC6
SOFTWARE
ARG A:405 , ARG B:161
BINDING SITE FOR RESIDUE EDO A 1962
34
DC7
SOFTWARE
MSE B:475 , HOH B:896
BINDING SITE FOR RESIDUE EDO B 814
35
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
36
DC9
SOFTWARE
PHE A:106
BINDING SITE FOR RESIDUE EDO A 1964
37
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
38
EC2
SOFTWARE
PRO A:237 , VAL A:310
BINDING SITE FOR RESIDUE IMD A 1966
39
EC3
SOFTWARE
ARG B:171 , ALA B:172 , GLY B:217 , HOH B:937
BINDING SITE FOR RESIDUE EDO B 815
40
EC4
SOFTWARE
PRO A:208 , LEU A:228 , PRO A:279 , HOH A:2002
BINDING SITE FOR RESIDUE IMD A 1967
41
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
42
EC6
SOFTWARE
ARG B:54 , TYR B:55 , ARG B:254 , ILE B:255 , THR B:270 , ASP B:272 , ARG B:317 , ARG B:332
BINDING SITE FOR RESIDUE 13P B 816
43
EC7
SOFTWARE
EDO A:1955 , GLN B:303 , EDO B:803
BINDING SITE FOR RESIDUE EDO B 817
44
EC8
SOFTWARE
GLU B:383
BINDING SITE FOR RESIDUE EDO B 818
45
EC9
SOFTWARE
TRP B:488 , GLU B:491 , TYR B:492
BINDING SITE FOR RESIDUE IMD B 819
46
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
47
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
48
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 not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: FAD_G3PDH_1 (A:9-26,B:9-26)
2: FAD_G3PDH_2 (A:352-362,B: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
2
A:9-26
B:9-26
2
FAD_G3PDH_2
PS00978
FAD-dependent glycerol-3-phosphate dehydrogenase signature 2.
GLPD_ECOLI
352-362
2
A:352-362
B: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.
SCOP Domains
(0, 0)
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Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
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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)
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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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