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2QCU
Biol. Unit 1
Info
Asym.Unit (189 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (92 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLYCEROL-3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI
Authors
:
J. I. Yeh, U. Chinte, S. Du
Date
:
19 Jun 07 (Deposition) - 15 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Glycerol-3-Phoshate Dehydrogenase, 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
(7, 27)
Info
All Hetero Components
1a: B-OCTYLGLUCOSIDE (BOGa)
1b: B-OCTYLGLUCOSIDE (BOGb)
1c: B-OCTYLGLUCOSIDE (BOGc)
1d: B-OCTYLGLUCOSIDE (BOGd)
1e: B-OCTYLGLUCOSIDE (BOGe)
1f: B-OCTYLGLUCOSIDE (BOGf)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
4a: IMIDAZOLE (IMDa)
4b: IMIDAZOLE (IMDb)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
7a: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMa)
7b: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMb)
7c: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BOG
4
Ligand/Ion
B-OCTYLGLUCOSIDE
2
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
3
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
4
IMD
2
Ligand/Ion
IMIDAZOLE
5
PO4
1
Ligand/Ion
PHOSPHATE ION
6
SO4
2
Ligand/Ion
SULFATE ION
7
TAM
2
Ligand/Ion
TRIS(HYDROXYETHYL)AMINOMETHANE
[
close Hetero Component info
]
Sites
(31, 31)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC8 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC4 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC7 (SOFTWARE)
13: BC8 (SOFTWARE)
14: BC9 (SOFTWARE)
15: CC1 (SOFTWARE)
16: CC2 (SOFTWARE)
17: CC3 (SOFTWARE)
18: CC4 (SOFTWARE)
19: CC5 (SOFTWARE)
20: CC6 (SOFTWARE)
21: CC7 (SOFTWARE)
22: CC8 (SOFTWARE)
23: CC9 (SOFTWARE)
24: DC1 (SOFTWARE)
25: DC2 (SOFTWARE)
26: DC3 (SOFTWARE)
27: DC4 (SOFTWARE)
28: DC5 (SOFTWARE)
29: DC6 (SOFTWARE)
30: DC8 (SOFTWARE)
31: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:99
BINDING SITE FOR RESIDUE BOG A 700
02
AC2
SOFTWARE
TRP A:99 , ARG A:102 , ARG A:137 , BOG A:800
BINDING SITE FOR RESIDUE BOG A 701
03
AC3
SOFTWARE
HIS A:91 , PRO A:93 , PRO A:97 , ALA A:98 , GLU A:134 , LYS A:136 , BOG A:701
BINDING SITE FOR RESIDUE BOG A 800
04
AC4
SOFTWARE
LEU A:53 , ARG A:54 , LEU A:56 , GLU A:57 , TYR A:59 , ARG A:96 , ILE A:101 , GLY A:104 , MET A:107
BINDING SITE FOR RESIDUE BOG A 801
05
AC6
SOFTWARE
TYR A:59 , ARG A:62 , ARG B:102 , THR B:121 , GLY B:122 , BOG B:700
BINDING SITE FOR RESIDUE BOG B 800
06
AC7
SOFTWARE
VAL A:310 , TRP A:311 , TRP A:468 , GLY A:474 , MET A:475
BINDING SITE FOR RESIDUE SO4 A 802
07
AC8
SOFTWARE
HIS A:80 , PHE A:83 , ASP A:394 , ARG A:419 , HOH A:1031
BINDING SITE FOR RESIDUE SO4 A 803
08
BC1
SOFTWARE
ARG A:161 , HOH A:942 , TYR B:398 , ARG B:401 , LEU B:402 , ARG B:405 , GLU B:426
BINDING SITE FOR RESIDUE SO4 B 802
09
BC2
SOFTWARE
ARG A:54 , TYR A:55 , ARG A:317 , ARG A:332 , LYS A:354 , HOH A:897 , HOH A:973 , HOH A:989 , HOH A:1057
BINDING SITE FOR RESIDUE PO4 A 804
10
BC4
SOFTWARE
ILE A:9 , GLY A:10 , GLY A:11 , GLY A:12 , ILE A:13 , ASN A:14 , GLU A:33 , ALA A:34 , CYS A:39 , ALA A:40 , THR A:41 , SER A:42 , ALA A:44 , SER A:45 , SER A:46 , LYS A:47 , LEU A:48 , HIS A:50 , ALA A:172 , THR A:206 , GLY A:207 , PRO A:208 , PHE A:213 , GLY A:231 , THR A:270 , ARG A:317 , GLY A:353 , LYS A:354 , LEU A:355 , THR A:356 , EDO A:806 , HOH A:824 , HOH A:825 , HOH A:1052
BINDING SITE FOR RESIDUE FAD A 600
11
BC6
SOFTWARE
ALA A:23 , GLY A:24 , LYS A:162 , HOH A:942 , HOH A:1056 , ARG B:401 , ARG B:404 , HOH B:971
BINDING SITE FOR RESIDUE TAM A 805
12
BC7
SOFTWARE
ALA A:34 , ARG A:171 , LYS A:280 , FAD A:600
BINDING SITE FOR RESIDUE EDO A 806
13
BC8
SOFTWARE
HIS A:444 , GLU A:445 , GLN A:473 , EDO A:811
BINDING SITE FOR RESIDUE IMD A 807
14
BC9
SOFTWARE
SER A:43 , TRP A:311 , TRP A:468 , EDO A:812 , HOH A:826 , HOH A:832 , HOH A:1034 , HOH A:1035
BINDING SITE FOR RESIDUE EDO A 808
15
CC1
SOFTWARE
GLN A:303 , EDO A:815 , HOH A:964 , HOH A:1039 , EDO B:805
BINDING SITE FOR RESIDUE EDO A 809
16
CC2
SOFTWARE
ARG A:306 , ILE A:309
BINDING SITE FOR RESIDUE EDO A 810
17
CC3
SOFTWARE
HIS A:416 , THR A:471 , LYS A:472 , GLN A:473 , TRP A:476 , IMD A:807 , HOH A:872
BINDING SITE FOR RESIDUE EDO A 811
18
CC4
SOFTWARE
TRP A:311 , TRP A:468 , EDO A:808
BINDING SITE FOR RESIDUE EDO A 812
19
CC5
SOFTWARE
GLU A:448
BINDING SITE FOR RESIDUE EDO A 813
20
CC6
SOFTWARE
GLU A:440 , ASP A:441
BINDING SITE FOR RESIDUE EDO A 814
21
CC7
SOFTWARE
ASN A:294 , ASN A:297 , THR A:298 , EDO A:809 , HOH A:928
BINDING SITE FOR RESIDUE EDO A 815
22
CC8
SOFTWARE
ASN A:294 , HOH A:947 , SER B:305 , ARG B:306 , HOH B:839
BINDING SITE FOR RESIDUE EDO A 816
23
CC9
SOFTWARE
ARG A:254 , THR A:271 , ASP A:272 , TAM A:823
BINDING SITE FOR RESIDUE EDO A 817
24
DC1
SOFTWARE
ALA A:40 , THR A:41 , PRO A:279 , LYS A:280 , VAL A:282 , GLY A:315 , VAL A:316 , HOH A:1043
BINDING SITE FOR RESIDUE EDO A 818
25
DC2
SOFTWARE
ARG A:404 , ALA B:23 , GLY B:24 , HOH B:1025
BINDING SITE FOR RESIDUE EDO A 819
26
DC3
SOFTWARE
ASP A:397 , ARG A:404 , HOH A:939 , HOH A:969
BINDING SITE FOR RESIDUE EDO A 820
27
DC4
SOFTWARE
GLN A:157 , ASN A:424 , LEU A:427 , TYR A:453 , EDO A:822 , HOH A:1066 , HOH B:957
BINDING SITE FOR RESIDUE IMD A 821
28
DC5
SOFTWARE
GLN A:157 , HIS A:457 , TRP A:459 , IMD A:821 , HOH A:1063 , ARG B:405
BINDING SITE FOR RESIDUE EDO A 822
29
DC6
SOFTWARE
ASP A:272 , VAL A:273 , GLU A:274 , GLU A:285 , SER A:287 , GLU A:288 , EDO A:817 , GLU B:285 , SER B:287 , HOH B:924
BINDING SITE FOR RESIDUE TAM A 823
30
DC8
SOFTWARE
EDO A:809 , LEU B:293 , ASN B:294 , ASN B:297 , HOH B:860
BINDING SITE FOR RESIDUE EDO B 805
31
EC4
SOFTWARE
ARG A:405 , GLU A:426 , GLN B:157 , VAL B:160 , ARG B:161 , PRO B:387 , ASN B:424 , HIS B:457 , HOH B:1054
BINDING SITE FOR RESIDUE TAM B 810
[
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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Label:
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_2qcuB01 (B:5-359)
1b: PFAM_DAO_2qcuB02 (B:5-359)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
DAO
(25)
Escherichia coli (strain K12)
(6)
1a
DAO-2qcuB01
B:5-359
1b
DAO-2qcuB02
B:5-359
[
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]
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Asymmetric Unit 1
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