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2QJN
Biol. Unit 3
Info
Asym.Unit (268 KB)
Biol.Unit 1 (134 KB)
Biol.Unit 2 (134 KB)
Biol.Unit 3 (519 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF D-MANNONATE DEHYDRATASE FROM NOVOSPHINGOBIUM AROMATICIVORANS COMPLEXED WITH MG AND 2-KETO-3-DEOXY-D-GLUCONATE
Authors
:
A. A. Fedorov, E. V. Fedorov, J. F. Rakus, J. E. Vick, J. A. Gerlt, S. C. Alm
Date
:
08 Jul 07 (Deposition) - 30 Oct 07 (Release) - 13 Jul 11 (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)
Biol. Unit 3: A,B,C,D (2x)
Keywords
:
D-Mannonate Dehydratase, Enolase Superfamily, Lyase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
J. F. Rakus, A. A. Fedorov, E. V. Fedorov, M. E. Glasner, J. E. Vick, P. C. Babbitt, S. C. Almo, J. A. Gerlt
Evolution Of Enzymatic Activities In The Enolase Superfamily: D-Mannonate Dehydratase From Novosphingobium Aromaticivorans.
Biochemistry V. 46 12896 2007
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Hetero Components
(1, 8)
Info
All Hetero Components
1a: 2-KETO-3-DEOXYGLUCONATE (KDGa)
1b: 2-KETO-3-DEOXYGLUCONATE (KDGb)
1c: 2-KETO-3-DEOXYGLUCONATE (KDGc)
1d: 2-KETO-3-DEOXYGLUCONATE (KDGd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
KDG
8
Ligand/Ion
2-KETO-3-DEOXYGLUCONATE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:210 , GLU A:236 , GLU A:262 , KDG A:2001 , HOH A:2154
BINDING SITE FOR RESIDUE MG A 1001
2
AC2
SOFTWARE
ASP B:210 , GLU B:236 , GLU B:262 , KDG B:2002 , HOH B:2173
BINDING SITE FOR RESIDUE MG B 1002
3
AC3
SOFTWARE
ASP C:210 , GLU C:236 , GLU C:262 , KDG C:2003 , HOH C:2157
BINDING SITE FOR RESIDUE MG C 1003
4
AC4
SOFTWARE
ASP D:210 , GLU D:236 , GLU D:262 , KDG D:2004 , HOH D:2139
BINDING SITE FOR RESIDUE MG D 1004
5
AC5
SOFTWARE
ASN A:37 , HIS A:122 , ARG A:147 , ASP A:210 , HIS A:212 , GLU A:236 , GLU A:262 , ARG A:283 , HIS A:312 , ALA A:314 , ASP A:316 , GLU A:339 , LEU A:389 , TRP A:402 , MG A:1001 , HOH A:2054 , TRP B:76
BINDING SITE FOR RESIDUE KDG A 2001
6
AC6
SOFTWARE
TRP A:76 , ASN B:37 , HIS B:122 , ASP B:210 , HIS B:212 , GLU B:236 , GLU B:262 , ARG B:283 , HIS B:312 , ALA B:314 , ASP B:316 , GLU B:339 , LEU B:389 , TRP B:402 , MG B:1002 , HOH B:2028
BINDING SITE FOR RESIDUE KDG B 2002
7
AC7
SOFTWARE
ASN C:37 , HIS C:122 , ARG C:147 , ASP C:210 , HIS C:212 , GLU C:236 , GLU C:262 , ARG C:283 , HIS C:312 , ALA C:314 , ASP C:316 , GLU C:339 , MET C:341 , TRP C:402 , MG C:1003 , HOH C:2007 , TRP D:76
BINDING SITE FOR RESIDUE KDG C 2003
8
AC8
SOFTWARE
TYR C:75 , TRP C:76 , ASN D:37 , ARG D:147 , ASP D:210 , HIS D:212 , GLU D:236 , GLU D:262 , ARG D:283 , HIS D:312 , ALA D:314 , ASP D:316 , GLU D:339 , MET D:341 , LEU D:389 , TRP D:402 , MG D:1004 , HOH D:2013
BINDING SITE FOR RESIDUE KDG D 2004
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: MR_MLE_1 (A:85-110,B:85-110,C:85-110,D:85-11...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MR_MLE_1
PS00908
Mandelate racemase / muconate lactonizing enzyme family signature 1.
MAND_NOVAD
85-110
8
A:85-110
B:85-110
C:85-110
D:85-110
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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.
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SCOP Domains
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2qjnA01 (A:1-104,A:367-402)
1b: CATH_2qjnB01 (B:1-104,B:367-402)
1c: CATH_2qjnC01 (C:1-104,C:367-402)
1d: CATH_2qjnD01 (D:1-104,D:367-402)
2a: CATH_2qjnA02 (A:105-366)
2b: CATH_2qjnB02 (B:105-366)
2c: CATH_2qjnD02 (D:105-366)
2d: CATH_2qjnC02 (C:105-366)
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Organisms
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(
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Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
Enolase-like, N-terminal domain
(130)
Novosphingobium aromaticivorans. Organism_taxid: 48935.
(3)
1a
2qjnA01
A:1-104,A:367-402
1b
2qjnB01
B:1-104,B:367-402
1c
2qjnC01
C:1-104,C:367-402
1d
2qjnD01
D:1-104,D:367-402
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Enolase superfamily
(142)
Novosphingobium aromaticivorans. Organism_taxid: 48935.
(3)
2a
2qjnA02
A:105-366
2b
2qjnB02
B:105-366
2c
2qjnD02
D:105-366
2d
2qjnC02
C:105-366
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Pfam Domains
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Show PDB file:
Asym.Unit (268 KB)
Header - Asym.Unit
Biol.Unit 1 (134 KB)
Header - Biol.Unit 1
Biol.Unit 2 (134 KB)
Header - Biol.Unit 2
Biol.Unit 3 (519 KB)
Header - Biol.Unit 3
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