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1JDF
Asym. Unit
Info
Asym.Unit (302 KB)
Biol.Unit 1 (150 KB)
Biol.Unit 2 (152 KB)
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(1)
Title
:
GLUCARATE DEHYDRATASE FROM E.COLI N341D MUTANT
Authors
:
A. M. Gulick, B. K. Hubbard, J. A. Gerlt, I. Rayment
Date
:
13 Jun 01 (Deposition) - 05 Sep 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Tim Barrel, Alpha/Beta Barrel, Enolase Superfamily, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. M. Gulick, B. K. Hubbard, J. A. Gerlt, I. Rayment
Evolution Of Enzymatic Activities In The Enolase Superfamily: Identification Of The General Acid Catalyst In The Active Site Of D-Glucarate Dehydratase From Escherichia Coli.
Biochemistry V. 40 10054 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 16)
Info
All Hetero Components
1a: 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE (GLRa)
1b: 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE (GLRb)
1c: 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE (GLRc)
1d: 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE (GLRd)
2a: ISOPROPYL ALCOHOL (IPAa)
2b: ISOPROPYL ALCOHOL (IPAb)
2c: ISOPROPYL ALCOHOL (IPAc)
2d: ISOPROPYL ALCOHOL (IPAd)
2e: ISOPROPYL ALCOHOL (IPAe)
2f: ISOPROPYL ALCOHOL (IPAf)
2g: ISOPROPYL ALCOHOL (IPAg)
2h: ISOPROPYL ALCOHOL (IPAh)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GLR
4
Ligand/Ion
2,3-DIHYDROXY-5-OXO-HEXANEDIOATE
2
IPA
8
Ligand/Ion
ISOPROPYL ALCOHOL
3
MG
4
Ligand/Ion
MAGNESIUM ION
[
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Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:235 , GLU A:260 , ASN A:289 , GLR A:2510 , HOH A:4655
BINDING SITE FOR RESIDUE MG A 4500
02
AC2
SOFTWARE
ASP B:235 , GLU B:260 , ASN B:289 , GLR B:2511 , HOH B:4638
BINDING SITE FOR RESIDUE MG B 4501
03
AC3
SOFTWARE
ASP C:235 , GLU C:260 , ASN C:289 , GLR C:2512 , HOH C:4698
BINDING SITE FOR RESIDUE MG C 4502
04
AC4
SOFTWARE
ASP D:235 , GLU D:260 , ASN D:289 , GLR D:2513 , HOH D:4679
BINDING SITE FOR RESIDUE MG D 4503
05
AC5
SOFTWARE
ASN A:27 , HIS A:32 , THR A:103 , PHE A:104 , TYR A:150 , PHE A:152 , LYS A:205 , LYS A:207 , ASP A:235 , ASN A:237 , GLU A:260 , ASN A:289 , HIS A:339 , SER A:340 , ASP A:341 , HIS A:368 , ARG A:422 , MG A:4500 , HOH A:4625 , HOH A:4654 , HOH A:4753
BINDING SITE FOR RESIDUE GLR A 2510
06
AC6
SOFTWARE
ASN B:27 , HIS B:32 , THR B:103 , TYR B:150 , PHE B:152 , LYS B:205 , LYS B:207 , ASP B:235 , ASN B:237 , GLU B:260 , ASN B:289 , HIS B:339 , SER B:340 , ASP B:341 , HIS B:368 , ARG B:422 , MG B:4501 , HOH B:4562 , HOH B:4630
BINDING SITE FOR RESIDUE GLR B 2511
07
AC7
SOFTWARE
ASN C:27 , HIS C:32 , THR C:103 , TYR C:150 , PHE C:152 , LYS C:205 , LYS C:207 , ASP C:235 , ASN C:237 , GLU C:260 , ASN C:289 , HIS C:339 , SER C:340 , ASP C:341 , HIS C:368 , ARG C:422 , MG C:4502 , HOH C:4599 , HOH C:4650 , HOH C:4697
BINDING SITE FOR RESIDUE GLR C 2512
08
AC8
SOFTWARE
ASN D:27 , HIS D:32 , THR D:103 , PHE D:104 , TYR D:150 , PHE D:152 , LYS D:205 , LYS D:207 , ASP D:235 , ASN D:237 , GLU D:260 , ASN D:289 , HIS D:339 , SER D:340 , ASP D:341 , HIS D:368 , ARG D:422 , MG D:4503 , HOH D:4638 , HOH D:4647 , HOH D:4678
BINDING SITE FOR RESIDUE GLR D 2513
09
AC9
SOFTWARE
LEU A:302 , PHE A:332 , GLY C:299 , LEU C:302 , SER C:303 , HOH C:4699
BINDING SITE FOR RESIDUE IPA C 3601
10
BC1
SOFTWARE
LEU B:302 , PHE B:332 , HOH B:4603 , HOH B:4725 , GLY D:299 , LEU D:302 , SER D:303 , HOH D:4524 , HOH D:4810
BINDING SITE FOR RESIDUE IPA D 3602
11
BC2
SOFTWARE
GLY A:299 , LEU A:302 , SER A:303 , LEU C:302 , PHE C:332 , HOH C:4699
BINDING SITE FOR RESIDUE IPA A 3603
12
BC3
SOFTWARE
GLY B:299 , SER B:303 , HOH B:4603 , HOH B:4629 , LEU D:302 , PHE D:332 , HOH D:4518
BINDING SITE FOR RESIDUE IPA B 3604
13
BC4
SOFTWARE
ARG A:88 , ASP A:95 , ILE A:110 , HOH A:4713
BINDING SITE FOR RESIDUE IPA A 3605
14
BC5
SOFTWARE
ARG B:88 , ASP B:95 , THR B:109
BINDING SITE FOR RESIDUE IPA B 3606
15
BC6
SOFTWARE
ARG C:88 , ALA C:92 , ASP C:95 , THR C:109
BINDING SITE FOR RESIDUE IPA C 3607
16
BC7
SOFTWARE
ARG D:88 , ALA D:92 , ASP D:95 , HOH D:4623
BINDING SITE FOR RESIDUE IPA D 3608
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
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;
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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, 8)
Info
All SCOP Domains
1a: SCOP_d1jdfa2 (A:5-137)
1b: SCOP_d1jdfb2 (B:5-137)
1c: SCOP_d1jdfc2 (C:5-137)
1d: SCOP_d1jdfd2 (D:5-137)
2a: SCOP_d1jdfa1 (A:138-446)
2b: SCOP_d1jdfb1 (B:138-446)
2c: SCOP_d1jdfc1 (C:138-446)
2d: SCOP_d1jdfd1 (D:138-446)
View:
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Classes
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(
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(
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(
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Families
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)
(
)
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
:
Enolase N-terminal domain-like
(88)
Protein domain
:
D-glucarate dehydratase
(8)
Escherichia coli [TaxId: 562]
(7)
1a
d1jdfa2
A:5-137
1b
d1jdfb2
B:5-137
1c
d1jdfc2
C:5-137
1d
d1jdfd2
D:5-137
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
:
D-glucarate dehydratase
(8)
Escherichia coli [TaxId: 562]
(7)
2a
d1jdfa1
A:138-446
2b
d1jdfb1
B:138-446
2c
d1jdfc1
C:138-446
2d
d1jdfd1
D:138-446
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1jdfA01 (A:6-137,A:399-416)
1b: CATH_1jdfB01 (B:6-137,B:399-416)
1c: CATH_1jdfC01 (C:6-137,C:399-416)
1d: CATH_1jdfD01 (D:6-137,D:399-416)
2a: CATH_1jdfA02 (A:138-398)
2b: CATH_1jdfB02 (B:138-398)
2c: CATH_1jdfC02 (C:138-398)
2d: CATH_1jdfD02 (D:138-398)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
Enolase-like, N-terminal domain
(130)
Escherichia coli. Organism_taxid: 562.
(10)
1a
1jdfA01
A:6-137,A:399-416
1b
1jdfB01
B:6-137,B:399-416
1c
1jdfC01
C:6-137,C:399-416
1d
1jdfD01
D:6-137,D:399-416
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Enolase superfamily
(142)
Escherichia coli. Organism_taxid: 562.
(10)
2a
1jdfA02
A:138-398
2b
1jdfB02
B:138-398
2c
1jdfC02
C:138-398
2d
1jdfD02
D:138-398
[
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]
Pfam Domains
(0, 0)
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