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2FLI
Biol. Unit 1
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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
)
[
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Hetero Components
(1, 6)
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
6
Ligand/Ion
D-XYLITOL-5-PHOSPHATE
2
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: BC6 (SOFTWARE)
10: BC7 (SOFTWARE)
11: BC8 (SOFTWARE)
12: BC9 (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
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
08
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
09
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
10
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
11
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
12
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
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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
(, 0)
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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.
(no "Exon" information available for biological units yet)
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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)
(
)
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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