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Biol. Unit 3
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Asym.Unit (270 KB)
Biol.Unit 1 (263 KB)
Biol.Unit 2 (264 KB)
Biol.Unit 3, α-C (1.0 MB)
Biol.Unit 3 (1.0 MB)
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Title
:
CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS COMPLEXED WITH MAGNESIUM, L-XYLAROHYDROXAMATE AND L-LYXAROHYDROXAMATE
Authors
:
A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo
Date
:
09 Sep 13 (Deposition) - 18 Sep 13 (Release) - 18 Sep 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: A,B (4x)
Keywords
:
Enolase Fold, D-Glucarate Dehydratase, L-Xylarohydroxamate, L- Lyxarohydroxamate, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. A. Fedorov, E. V. Fedorov, A. Sakai, J. A. Gerlt, S. C. Almo
Crystal Structure Of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed With Magnesium, L-Xylarohydroxamate And L-Lyxarohydroxamate
To Be Published
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Hetero Components
(3, 20)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
2a: (2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYD... (LLHa)
2b: (2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYD... (LLHb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
4a: TRIETHYLENE GLYCOL (PGEa)
5a: XYLAROHYDROXAMATE (XYHa)
5b: XYLAROHYDROXAMATE (XYHb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
LLH
8
Ligand/Ion
(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
PGE
4
Ligand/Ion
TRIETHYLENE GLYCOL
5
XYH
8
Ligand/Ion
XYLAROHYDROXAMATE
[
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Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:335 , HOH A:669 , HOH A:698 , HOH A:854 , HOH A:857 , HOH A:859
BINDING SITE FOR RESIDUE MG A 401
02
AC2
SOFTWARE
ASP A:206 , GLU A:232 , GLU A:258 , XYH A:404 , LLH A:405 , HOH A:794
BINDING SITE FOR RESIDUE MG A 402
03
AC3
SOFTWARE
SER A:247 , LEU A:250 , HOH A:795 , HOH A:796 , HOH A:797 , HOH A:798
BINDING SITE FOR RESIDUE MG A 403
04
AC4
SOFTWARE
HIS A:24 , CYS A:139 , LYS A:169 , HIS A:171 , ASP A:206 , HIS A:209 , GLU A:232 , GLU A:258 , ARG A:280 , HIS A:309 , GLU A:329 , MG A:402 , HOH A:543 , HOH A:548 , HOH A:794 , HOH A:851 , ARG B:90
BINDING SITE FOR RESIDUE XYH A 404
05
AC5
SOFTWARE
HIS A:24 , LYS A:169 , HIS A:171 , ASP A:206 , HIS A:209 , GLU A:232 , GLU A:258 , ARG A:280 , HIS A:309 , GLU A:329 , MG A:402 , HOH A:543 , HOH A:548 , HOH A:794 , HOH A:840 , HOH A:851 , ARG B:90
BINDING SITE FOR RESIDUE LLH A 405
06
AC6
SOFTWARE
ARG A:163 , ARG A:330 , ASP A:340 , LEU A:349 , PRO A:352 , MET A:353
BINDING SITE FOR RESIDUE CL A 406
07
AC7
SOFTWARE
ARG A:128 , VAL A:131 , LEU A:132 , HOH A:545
BINDING SITE FOR RESIDUE CL A 407
08
AC8
SOFTWARE
LYS A:347 , PHE A:373 , THR A:374
BINDING SITE FOR RESIDUE CL A 408
09
AC9
SOFTWARE
MET A:1 , ASP A:74
BINDING SITE FOR RESIDUE CL A 409
10
BC1
SOFTWARE
MET A:1 , ARG A:76
BINDING SITE FOR RESIDUE CL A 410
11
BC2
SOFTWARE
GLN A:238 , ALA A:261 , HOH A:869 , GLN B:238 , ALA B:261 , GLY B:262 , HOH B:644
BINDING SITE FOR RESIDUE PGE A 411
12
BC3
SOFTWARE
GLU A:338 , PRO B:335 , HOH B:676 , HOH B:804 , HOH B:842 , HOH B:856 , HOH B:857
BINDING SITE FOR RESIDUE MG B 401
13
BC4
SOFTWARE
ASP B:206 , GLU B:232 , GLU B:258 , XYH B:404 , LLH B:405 , HOH B:786
BINDING SITE FOR RESIDUE MG B 402
14
BC5
SOFTWARE
SER B:247 , LEU B:250 , HOH B:787 , HOH B:788 , HOH B:789 , HOH B:790
BINDING SITE FOR RESIDUE MG B 403
15
BC6
SOFTWARE
ARG A:90 , HIS B:24 , LYS B:169 , HIS B:171 , ASP B:206 , HIS B:209 , GLU B:232 , GLU B:258 , ARG B:280 , HIS B:309 , GLU B:329 , MG B:402 , HOH B:545 , HOH B:568 , HOH B:786 , HOH B:855
BINDING SITE FOR RESIDUE XYH B 404
16
BC7
SOFTWARE
ARG A:90 , HIS B:24 , LYS B:169 , HIS B:171 , ASP B:206 , HIS B:209 , GLU B:232 , GLU B:258 , ARG B:280 , HIS B:309 , GLU B:329 , MG B:402 , HOH B:545 , HOH B:568 , HOH B:786 , HOH B:835 , HOH B:855
BINDING SITE FOR RESIDUE LLH B 405
17
BC8
SOFTWARE
ARG B:163 , ARG B:330 , LEU B:349 , MET B:353
BINDING SITE FOR RESIDUE CL B 406
18
BC9
SOFTWARE
HOH A:676 , PRO B:59 , HIS B:60 , HOH B:841
BINDING SITE FOR RESIDUE CL B 407
19
CC1
SOFTWARE
ARG B:128 , VAL B:131 , LEU B:132
BINDING SITE FOR RESIDUE CL B 408
20
CC2
SOFTWARE
MET B:1 , ASP B:74
BINDING SITE FOR RESIDUE CL B 409
21
CC3
SOFTWARE
MET B:1 , ARG B:76
BINDING SITE FOR RESIDUE CL B 410
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d4mmwa1 (A:1-126)
1b: SCOP_d4mmwb1 (B:1-126)
2a: SCOP_d4mmwa2 (A:127-381)
2b: SCOP_d4mmwb2 (B:127-381)
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Protein Domains
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)
(
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Organisms
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)
(
)
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)
Agrobacterium tumefaciens [TaxId: 176299]
(6)
1a
d4mmwa1
A:1-126
1b
d4mmwb1
B:1-126
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)
Agrobacterium tumefaciens [TaxId: 176299]
(4)
2a
d4mmwa2
A:127-381
2b
d4mmwb2
B:127-381
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
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Sorry, no Info available
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