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2FLI
Asym. Unit
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Asym.Unit (426 KB)
Biol.Unit 1 (215 KB)
Biol.Unit 2 (213 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF D-RIBULOSE 5-PHOSPHATE 3-EPIMERASE FROM STREPTOCOCUS PYOGENES COMPLEXED WITH D-XYLITOL 5-PHOSPHATE
Authors
:
A. A. Fedorov, E. V. Fedorov, J. Akana, J. A. Gerlt, S. C. Almo
Date
:
06 Jan 06 (Deposition) - 07 Mar 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
D-Ribulose 5-Phosphate 3-Epimerase, (Beta/Alpha)8-Barrel, D- Xylitol 5-Phosphate, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Akana, A. A. Fedorov, E. Fedorov, W. R. Novak, P. C. Babbitt, S. C. Almo, J. A. Gerlt
D-Ribulose 5-Phosphate 3-Epimerase: Functional And Structural Relationships To Members Of The Ribulose-Phosphate Binding (Beta/Alpha)(8)-Barrel Superfamily(, ).
Biochemistry V. 45 2493 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 24)
Info
All Hetero Components
1a: D-XYLITOL-5-PHOSPHATE (DX5a)
1b: D-XYLITOL-5-PHOSPHATE (DX5b)
1c: D-XYLITOL-5-PHOSPHATE (DX5c)
1d: D-XYLITOL-5-PHOSPHATE (DX5d)
1e: D-XYLITOL-5-PHOSPHATE (DX5e)
1f: D-XYLITOL-5-PHOSPHATE (DX5f)
1g: D-XYLITOL-5-PHOSPHATE (DX5g)
1h: D-XYLITOL-5-PHOSPHATE (DX5h)
1i: D-XYLITOL-5-PHOSPHATE (DX5i)
1j: D-XYLITOL-5-PHOSPHATE (DX5j)
1k: D-XYLITOL-5-PHOSPHATE (DX5k)
1l: D-XYLITOL-5-PHOSPHATE (DX5l)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
2i: ZINC ION (ZNi)
2j: ZINC ION (ZNj)
2k: ZINC ION (ZNk)
2l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DX5
12
Ligand/Ion
D-XYLITOL-5-PHOSPHATE
2
ZN
12
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:34 , ASP A:36 , HIS A:67 , ASP A:176 , DX5 A:1901
BINDING SITE FOR RESIDUE ZN A 1981
02
AC2
SOFTWARE
HIS B:34 , ASP B:36 , HIS B:67 , ASP B:176 , DX5 B:1902
BINDING SITE FOR RESIDUE ZN B 1982
03
AC3
SOFTWARE
HIS C:34 , ASP C:36 , HIS C:67 , ASP C:176 , DX5 C:1903
BINDING SITE FOR RESIDUE ZN C 1983
04
AC4
SOFTWARE
HIS D:34 , ASP D:36 , HIS D:67 , ASP D:176 , DX5 D:1904
BINDING SITE FOR RESIDUE ZN D 1984
05
AC5
SOFTWARE
HIS E:34 , ASP E:36 , HIS E:67 , ASP E:176 , DX5 E:1905
BINDING SITE FOR RESIDUE ZN E 1985
06
AC6
SOFTWARE
HIS F:34 , ASP F:36 , HIS F:67 , ASP F:176 , DX5 F:1906
BINDING SITE FOR RESIDUE ZN F 1986
07
AC7
SOFTWARE
HIS G:34 , ASP G:36 , HIS G:67 , ASP G:176 , DX5 G:1911
BINDING SITE FOR RESIDUE ZN G 1991
08
AC8
SOFTWARE
HIS H:34 , ASP H:36 , HIS H:67 , ASP H:176 , DX5 H:1912
BINDING SITE FOR RESIDUE ZN H 1992
09
AC9
SOFTWARE
HIS I:34 , ASP I:36 , HIS I:67 , ASP I:176 , DX5 I:1913
BINDING SITE FOR RESIDUE ZN I 1993
10
BC1
SOFTWARE
HIS J:34 , ASP J:36 , HIS J:67 , ASP J:176 , DX5 J:1914
BINDING SITE FOR RESIDUE ZN J 1994
11
BC2
SOFTWARE
HIS K:34 , ASP K:36 , HIS K:67 , ASP K:176 , DX5 K:1915
BINDING SITE FOR RESIDUE ZN K 1995
12
BC3
SOFTWARE
HIS L:34 , ASP L:36 , HIS L:67 , ASP L:176 , DX5 L:1916
BINDING SITE FOR RESIDUE ZN L 1996
13
BC4
SOFTWARE
SER A:9 , LEU A:11 , HIS A:34 , ASP A:36 , HIS A:67 , MET A:69 , PRO A:142 , GLY A:143 , PHE A:144 , GLY A:145 , GLY A:146 , ASP A:176 , GLY A:177 , GLY A:178 , ALA A:197 , GLY A:198 , SER A:199 , ZN A:1981 , HOH A:1991 , HOH A:2020 , HOH A:2027 , HOH A:2035 , HOH A:2039
BINDING SITE FOR RESIDUE DX5 A 1901
14
BC5
SOFTWARE
SER B:9 , LEU B:11 , HIS B:34 , ASP B:36 , MET B:69 , PRO B:142 , GLY B:143 , PHE B:144 , GLY B:145 , GLY B:146 , ASP B:176 , GLY B:177 , GLY B:178 , GLY B:198 , SER B:199 , ZN B:1982 , HOH B:1987 , HOH B:1994 , HOH B:2001 , HOH B:2002 , HOH B:2024
BINDING SITE FOR RESIDUE DX5 B 1902
15
BC6
SOFTWARE
SER C:9 , LEU C:11 , HIS C:34 , ASP C:36 , MET C:38 , HIS C:67 , MET C:69 , PRO C:142 , GLY C:143 , PHE C:144 , GLY C:145 , GLY C:146 , ASP C:176 , GLY C:177 , GLY C:178 , ALA C:197 , GLY C:198 , SER C:199 , ZN C:1983 , HOH C:1990 , HOH C:1994 , HOH C:1995 , HOH C:2036 , HOH C:2041
BINDING SITE FOR RESIDUE DX5 C 1903
16
BC7
SOFTWARE
SER D:9 , LEU D:11 , HIS D:34 , ASP D:36 , MET D:69 , PRO D:142 , GLY D:143 , PHE D:144 , GLY D:145 , GLY D:146 , ASP D:176 , GLY D:177 , GLY D:178 , VAL D:196 , ALA D:197 , GLY D:198 , SER D:199 , ZN D:1984 , HOH D:1993 , HOH D:2003 , HOH D:2005 , HOH D:2028
BINDING SITE FOR RESIDUE DX5 D 1904
17
BC8
SOFTWARE
SER E:9 , LEU E:11 , HIS E:34 , ASP E:36 , HIS E:67 , MET E:69 , PRO E:142 , GLY E:143 , PHE E:144 , GLY E:145 , GLY E:146 , ASP E:176 , GLY E:177 , GLY E:178 , GLY E:198 , SER E:199 , ZN E:1985 , HOH E:1997 , HOH E:2002 , HOH E:2034 , HOH E:2046
BINDING SITE FOR RESIDUE DX5 E 1905
18
BC9
SOFTWARE
SER F:9 , LEU F:11 , HIS F:34 , ASP F:36 , MET F:38 , MET F:69 , PRO F:142 , GLY F:143 , PHE F:144 , GLY F:145 , GLY F:146 , ASP F:176 , GLY F:177 , GLY F:178 , ALA F:197 , GLY F:198 , SER F:199 , ZN F:1986 , HOH F:1993 , HOH F:2002 , HOH F:2016 , HOH F:2031
BINDING SITE FOR RESIDUE DX5 F 1906
19
CC1
SOFTWARE
SER G:9 , LEU G:11 , HIS G:34 , ASP G:36 , MET G:38 , MET G:69 , PRO G:142 , GLY G:143 , PHE G:144 , GLY G:145 , GLY G:146 , ASP G:176 , GLY G:177 , GLY G:178 , GLY G:198 , SER G:199 , ZN G:1991 , HOH G:1992 , HOH G:2023 , HOH G:2033 , HOH G:2042
BINDING SITE FOR RESIDUE DX5 G 1911
20
CC2
SOFTWARE
SER H:9 , LEU H:11 , HIS H:34 , ASP H:36 , MET H:38 , HIS H:67 , MET H:69 , PRO H:142 , GLY H:143 , PHE H:144 , GLY H:145 , GLY H:146 , ASP H:176 , GLY H:177 , GLY H:178 , ALA H:197 , GLY H:198 , SER H:199 , ZN H:1992 , HOH H:1993 , HOH H:1998 , HOH H:2003 , HOH H:2007 , HOH H:2040
BINDING SITE FOR RESIDUE DX5 H 1912
21
CC3
SOFTWARE
SER I:9 , LEU I:11 , ASP I:36 , PRO I:142 , GLY I:143 , PHE I:144 , GLY I:145 , GLY I:146 , ASP I:176 , GLY I:177 , GLY I:178 , GLY I:198 , SER I:199 , ZN I:1993 , HOH I:2000 , HOH I:2003 , HOH I:2004 , HOH I:2026
BINDING SITE FOR RESIDUE DX5 I 1913
22
CC4
SOFTWARE
SER J:9 , LEU J:11 , HIS J:34 , ASP J:36 , HIS J:67 , MET J:69 , PRO J:142 , GLY J:143 , PHE J:144 , GLY J:145 , GLY J:146 , ASP J:176 , GLY J:177 , GLY J:178 , ALA J:197 , GLY J:198 , SER J:199 , ZN J:1994 , HOH J:1997 , HOH J:2000 , HOH J:2015 , HOH J:2023 , HOH J:2074
BINDING SITE FOR RESIDUE DX5 J 1914
23
CC5
SOFTWARE
SER K:9 , LEU K:11 , HIS K:34 , ASP K:36 , MET K:69 , PRO K:142 , GLY K:143 , PHE K:144 , GLY K:145 , GLY K:146 , ASP K:176 , GLY K:177 , GLY K:178 , GLY K:198 , SER K:199 , ZN K:1995 , HOH K:2005 , HOH K:2015 , HOH K:2037 , HOH K:2052
BINDING SITE FOR RESIDUE DX5 K 1915
24
CC6
SOFTWARE
SER L:9 , LEU L:11 , ASP L:36 , MET L:69 , PRO L:142 , GLY L:143 , PHE L:144 , GLY L:145 , GLY L:146 , ASP L:176 , GLY L:177 , GLY L:178 , ALA L:197 , GLY L:198 , SER L:199 , ZN L:1996 , HOH L:2009 , HOH L:2016 , HOH L:2047
BINDING SITE FOR RESIDUE DX5 L 1916
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
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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
(2, 12)
Info
All SCOP Domains
1a: SCOP_d2flib_ (B:)
1b: SCOP_d2flic_ (C:)
1c: SCOP_d2flil_ (L:)
1d: SCOP_d2flid_ (D:)
1e: SCOP_d2flie_ (E:)
1f: SCOP_d2flif_ (F:)
1g: SCOP_d2flig_ (G:)
1h: SCOP_d2flih_ (H:)
1i: SCOP_d2flii_ (I:)
1j: SCOP_d2flij_ (J:)
1k: SCOP_d2flik_ (K:)
2a: SCOP_d2flia1 (A:3-219)
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(
)
(
)
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)
(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Ribulose-phoshate binding barrel
(356)
Family
:
automated matches
(38)
Protein domain
:
automated matches
(38)
Streptococcus pyogenes [TaxId: 1314]
(1)
1a
d2flib_
B:
1b
d2flic_
C:
1c
d2flil_
L:
1d
d2flid_
D:
1e
d2flie_
E:
1f
d2flif_
F:
1g
d2flig_
G:
1h
d2flih_
H:
1i
d2flii_
I:
1j
d2flij_
J:
1k
d2flik_
K:
Family
:
D-ribulose-5-phosphate 3-epimerase
(6)
Protein domain
:
D-ribulose-5-phosphate 3-epimerase
(6)
Streptococcus pyogenes [TaxId: 1314]
(1)
2a
d2flia1
A:3-219
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2fliC00 (C:2-220)
1b: CATH_2fliG00 (G:2-219)
1c: CATH_2fliH00 (H:3-218)
1d: CATH_2fliK00 (K:3-218)
1e: CATH_2fliJ00 (J:2-219)
1f: CATH_2fliL00 (L:3-220)
1g: CATH_2fliA00 (A:3-219)
1h: CATH_2fliB00 (B:2-218)
1i: CATH_2fliD00 (D:2-218)
1j: CATH_2fliI00 (I:3-219)
1k: CATH_2fliE00 (E:3-218)
1l: CATH_2fliF00 (F:3-218)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Streptococcus pyogenes. Organism_taxid: 1314.
(2)
1a
2fliC00
C:2-220
1b
2fliG00
G:2-219
1c
2fliH00
H:3-218
1d
2fliK00
K:3-218
1e
2fliJ00
J:2-219
1f
2fliL00
L:3-220
1g
2fliA00
A:3-219
1h
2fliB00
B:2-218
1i
2fliD00
D:2-218
1j
2fliI00
I:3-219
1k
2fliE00
E:3-218
1l
2fliF00
F:3-218
[
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Pfam Domains
(0, 0)
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Asym.Unit (426 KB)
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