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2DW7
Biol. Unit 7
Info
Asym.Unit (990 KB)
Biol.Unit 1 (133 KB)
Biol.Unit 2 (136 KB)
Biol.Unit 3 (135 KB)
Biol.Unit 4 (133 KB)
Biol.Unit 5 (134 KB)
Biol.Unit 6 (134 KB)
Biol.Unit 7 (134 KB)
Biol.Unit 8 (133 KB)
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Title
:
CRYSTAL STRUCTURE OF D-TARTRATE DEHYDRATASE FROM BRADYRHIZOBIUM JAPONICUM COMPLEXED WITH MG++ AND MESO-TARTRATE
Authors
:
A. A. Fedorov, E. V. Fedorov, W. S. Yew, B. M. Wood, J. A. Gerlt, S. C. Almo
Date
:
07 Aug 06 (Deposition) - 19 Dec 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: I,J (1x)
Biol. Unit 6: K,L (1x)
Biol. Unit 7: M,N (1x)
Biol. Unit 8: O,P (1x)
Keywords
:
D-Tartrate Dehydratase, Enolase Superfamily, Meso-Tartrate, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. S. Yew, A. A. Fedorov, E. V. Fedorov, B. M. Wood, S. C. Almo, J. A. Gerlt
Evolution Of Enzymatic Activities In The Enolase Superfamily: D-Tartrate Dehydratase From Bradyrhizobium Japonicum
Biochemistry V. 45 14598 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
1i: MAGNESIUM ION (MGi)
1j: MAGNESIUM ION (MGj)
1k: MAGNESIUM ION (MGk)
1l: MAGNESIUM ION (MGl)
1m: MAGNESIUM ION (MGm)
1n: MAGNESIUM ION (MGn)
1o: MAGNESIUM ION (MGo)
1p: MAGNESIUM ION (MGp)
2a: S,R MESO-TARTARIC ACID (SRTa)
2b: S,R MESO-TARTARIC ACID (SRTb)
2c: S,R MESO-TARTARIC ACID (SRTc)
2d: S,R MESO-TARTARIC ACID (SRTd)
2e: S,R MESO-TARTARIC ACID (SRTe)
2f: S,R MESO-TARTARIC ACID (SRTf)
2g: S,R MESO-TARTARIC ACID (SRTg)
2h: S,R MESO-TARTARIC ACID (SRTh)
2i: S,R MESO-TARTARIC ACID (SRTi)
2j: S,R MESO-TARTARIC ACID (SRTj)
2k: S,R MESO-TARTARIC ACID (SRTk)
2l: S,R MESO-TARTARIC ACID (SRTl)
2m: S,R MESO-TARTARIC ACID (SRTm)
2n: S,R MESO-TARTARIC ACID (SRTn)
2o: S,R MESO-TARTARIC ACID (SRTo)
2p: S,R MESO-TARTARIC ACID (SRTp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
SRT
2
Ligand/Ion
S,R MESO-TARTARIC ACID
[
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]
Sites
(4, 4)
Info
All Sites
1: BC4 (SOFTWARE)
2: BC5 (SOFTWARE)
3: DC2 (SOFTWARE)
4: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
BC4
SOFTWARE
ASP M:213 , GLU M:239 , GLU M:240 , GLU M:265 , SRT M:1013
BINDING SITE FOR RESIDUE MG M 2013
2
BC5
SOFTWARE
ASP N:213 , GLU N:239 , GLU N:265 , SRT N:1014
BINDING SITE FOR RESIDUE MG N 2014
3
DC2
SOFTWARE
ASN M:21 , PHE M:26 , ASN M:55 , TYR M:156 , LYS M:182 , LYS M:184 , ASP M:213 , ASN M:215 , GLU M:239 , GLU M:265 , HIS M:322 , GLU M:341 , TYR M:343 , MG M:2013 , LYS N:102
BINDING SITE FOR RESIDUE SRT M 1013
4
DC3
SOFTWARE
LYS M:102 , ASN N:21 , PHE N:26 , ASN N:55 , TYR N:156 , LYS N:182 , LYS N:184 , ASP N:213 , ASN N:215 , GLU N:239 , GLU N:265 , HIS N:322 , GLU N:341 , TYR N:343 , MG N:2014
BINDING SITE FOR RESIDUE SRT N 1014
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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
(2, 32)
Info
All SCOP Domains
1a: SCOP_d2dw7a2 (A:2-142)
1b: SCOP_d2dw7g2 (G:2-142)
1c: SCOP_d2dw7h2 (H:2-142)
1d: SCOP_d2dw7i2 (I:2-142)
1e: SCOP_d2dw7j2 (J:2-142)
1f: SCOP_d2dw7k2 (K:2-142)
1g: SCOP_d2dw7l2 (L:2-142)
1h: SCOP_d2dw7m2 (M:2-142)
1i: SCOP_d2dw7n2 (N:2-142)
1j: SCOP_d2dw7o2 (O:2-142)
1k: SCOP_d2dw7p2 (P:2-142)
1l: SCOP_d2dw7b2 (B:2-142)
1m: SCOP_d2dw7c2 (C:2-142)
1n: SCOP_d2dw7d2 (D:2-142)
1o: SCOP_d2dw7e2 (E:2-142)
1p: SCOP_d2dw7f2 (F:2-142)
2a: SCOP_d2dw7a1 (A:143-389)
2b: SCOP_d2dw7g1 (G:143-389)
2c: SCOP_d2dw7h1 (H:143-389)
2d: SCOP_d2dw7i1 (I:143-389)
2e: SCOP_d2dw7j1 (J:143-389)
2f: SCOP_d2dw7k1 (K:143-389)
2g: SCOP_d2dw7l1 (L:143-389)
2h: SCOP_d2dw7m1 (M:143-389)
2i: SCOP_d2dw7n1 (N:143-389)
2j: SCOP_d2dw7o1 (O:143-389)
2k: SCOP_d2dw7p1 (P:143-389)
2l: SCOP_d2dw7b1 (B:143-389)
2m: SCOP_d2dw7c1 (C:143-389)
2n: SCOP_d2dw7d1 (D:143-389)
2o: SCOP_d2dw7e1 (E:143-389)
2p: SCOP_d2dw7f1 (F:143-389)
View:
Select:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Enolase N-terminal domain-like
(211)
Superfamily
:
Enolase N-terminal domain-like
(211)
Family
:
automated matches
(123)
Protein domain
:
automated matches
(123)
Bradyrhizobium japonicum [TaxId: 375]
(2)
1a
d2dw7a2
A:2-142
1b
d2dw7g2
G:2-142
1c
d2dw7h2
H:2-142
1d
d2dw7i2
I:2-142
1e
d2dw7j2
J:2-142
1f
d2dw7k2
K:2-142
1g
d2dw7l2
L:2-142
1h
d2dw7m2
M:2-142
1i
d2dw7n2
N:2-142
1j
d2dw7o2
O:2-142
1k
d2dw7p2
P:2-142
1l
d2dw7b2
B:2-142
1m
d2dw7c2
C:2-142
1n
d2dw7d2
D:2-142
1o
d2dw7e2
E:2-142
1p
d2dw7f2
F:2-142
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Enolase C-terminal domain-like
(212)
Family
:
D-glucarate dehydratase-like
(65)
Protein domain
:
automated matches
(16)
Bradyrhizobium japonicum [TaxId: 375]
(2)
2a
d2dw7a1
A:143-389
2b
d2dw7g1
G:143-389
2c
d2dw7h1
H:143-389
2d
d2dw7i1
I:143-389
2e
d2dw7j1
J:143-389
2f
d2dw7k1
K:143-389
2g
d2dw7l1
L:143-389
2h
d2dw7m1
M:143-389
2i
d2dw7n1
N:143-389
2j
d2dw7o1
O:143-389
2k
d2dw7p1
P:143-389
2l
d2dw7b1
B:143-389
2m
d2dw7c1
C:143-389
2n
d2dw7d1
D:143-389
2o
d2dw7e1
E:143-389
2p
d2dw7f1
F:143-389
[
close SCOP info
]
CATH Domains
(2, 32)
Info
all CATH domains
1a: CATH_2dw7A01 (A:2-129)
1b: CATH_2dw7E01 (E:2-129)
1c: CATH_2dw7F01 (F:2-129)
1d: CATH_2dw7G01 (G:2-129)
1e: CATH_2dw7H01 (H:2-129)
1f: CATH_2dw7I01 (I:2-129)
1g: CATH_2dw7J01 (J:2-129)
1h: CATH_2dw7K01 (K:2-129)
1i: CATH_2dw7L01 (L:2-129)
1j: CATH_2dw7M01 (M:2-129)
1k: CATH_2dw7N01 (N:2-129)
1l: CATH_2dw7O01 (O:2-129)
1m: CATH_2dw7P01 (P:2-129)
1n: CATH_2dw7B01 (B:2-129)
1o: CATH_2dw7C01 (C:2-129)
1p: CATH_2dw7D01 (D:2-129)
2a: CATH_2dw7A02 (A:130-389)
2b: CATH_2dw7I02 (I:130-389)
2c: CATH_2dw7J02 (J:130-389)
2d: CATH_2dw7K02 (K:130-389)
2e: CATH_2dw7L02 (L:130-389)
2f: CATH_2dw7M02 (M:130-389)
2g: CATH_2dw7N02 (N:130-389)
2h: CATH_2dw7O02 (O:130-389)
2i: CATH_2dw7P02 (P:130-389)
2j: CATH_2dw7B02 (B:130-389)
2k: CATH_2dw7C02 (C:130-389)
2l: CATH_2dw7D02 (D:130-389)
2m: CATH_2dw7E02 (E:130-389)
2n: CATH_2dw7F02 (F:130-389)
2o: CATH_2dw7G02 (G:130-389)
2p: CATH_2dw7H02 (H:130-389)
View:
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Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
Enolase-like, N-terminal domain
(130)
Bradyrhizobium japonicum. Organism_taxid: 375.
(3)
1a
2dw7A01
A:2-129
1b
2dw7E01
E:2-129
1c
2dw7F01
F:2-129
1d
2dw7G01
G:2-129
1e
2dw7H01
H:2-129
1f
2dw7I01
I:2-129
1g
2dw7J01
J:2-129
1h
2dw7K01
K:2-129
1i
2dw7L01
L:2-129
1j
2dw7M01
M:2-129
1k
2dw7N01
N:2-129
1l
2dw7O01
O:2-129
1m
2dw7P01
P:2-129
1n
2dw7B01
B:2-129
1o
2dw7C01
C:2-129
1p
2dw7D01
D:2-129
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Enolase superfamily
(142)
Bradyrhizobium japonicum. Organism_taxid: 375.
(3)
2a
2dw7A02
A:130-389
2b
2dw7I02
I:130-389
2c
2dw7J02
J:130-389
2d
2dw7K02
K:130-389
2e
2dw7L02
L:130-389
2f
2dw7M02
M:130-389
2g
2dw7N02
N:130-389
2h
2dw7O02
O:130-389
2i
2dw7P02
P:130-389
2j
2dw7B02
B:130-389
2k
2dw7C02
C:130-389
2l
2dw7D02
D:130-389
2m
2dw7E02
E:130-389
2n
2dw7F02
F:130-389
2o
2dw7G02
G:130-389
2p
2dw7H02
H:130-389
[
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]
Pfam Domains
(0, 0)
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Asym.Unit (990 KB)
Header - Asym.Unit
Biol.Unit 1 (133 KB)
Header - Biol.Unit 1
Biol.Unit 2 (136 KB)
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Biol.Unit 3 (135 KB)
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Biol.Unit 4 (133 KB)
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