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1ONW
Asym. Unit
Info
Asym.Unit (137 KB)
Biol.Unit 1 (510 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ISOASPARTYL DIPEPTIDASE FROM E. COLI
Authors
:
J. B. Thoden, R. Marti-Arbona, F. M. Raushel, H. M. Holden
Date
:
02 Mar 03 (Deposition) - 06 May 03 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (4x)
Keywords
:
Amidohydrolase, Hydrolase, Metalloprotease
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
J. B. Thoden, R. Marti-Arbona, F. M. Raushel, H. M. Holden
High Resolution X-Ray Structure Of Isoaspartyl Dipeptidase From Escherichia Coli
Biochemistry V. 42 4874 2003
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Hetero Components
(6, 14)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
4a: MAGNESIUM ION (MGa)
5a: SODIUM ION (NAa)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
3
Ligand/Ion
CHLORIDE ION
2
EDO
3
Ligand/Ion
1,2-ETHANEDIOL
3
KCX
2
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
MG
1
Ligand/Ion
MAGNESIUM ION
5
NA
1
Ligand/Ion
SODIUM ION
6
ZN
4
Ligand/Ion
ZINC ION
[
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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: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:68 , HIS A:70 , KCX A:162 , ASP A:285 , ZN A:801 , HOH A:841
BINDING SITE FOR RESIDUE ZN A 800
02
AC2
SOFTWARE
TYR A:137 , KCX A:162 , HIS A:201 , HIS A:230 , ZN A:800 , HOH A:841
BINDING SITE FOR RESIDUE ZN A 801
03
AC3
SOFTWARE
HIS B:68 , HIS B:70 , KCX B:162 , ASP B:285 , ZN B:803 , HOH B:864
BINDING SITE FOR RESIDUE ZN B 802
04
AC4
SOFTWARE
TYR B:137 , KCX B:162 , HIS B:201 , HIS B:230 , ZN B:802 , HOH B:864
BINDING SITE FOR RESIDUE ZN B 803
05
AC5
SOFTWARE
HOH B:978 , HOH B:979 , HOH B:991 , HOH B:1003
BINDING SITE FOR RESIDUE MG B 804
06
AC6
SOFTWARE
HOH A:886 , GLY B:193 , EDO B:807 , HOH B:869 , HOH B:998 , HOH B:1052 , HOH B:1107
BINDING SITE FOR RESIDUE NA B 805
07
AC7
SOFTWARE
LEU A:89 , GLY A:385 , HOH A:918
BINDING SITE FOR RESIDUE CL A 802
08
AC8
SOFTWARE
ALA B:88 , LEU B:89 , GLY B:385
BINDING SITE FOR RESIDUE CL B 806
09
AC9
SOFTWARE
ASP A:167 , HIS A:168 , ASP A:204
BINDING SITE FOR RESIDUE CL A 803
10
BC1
SOFTWARE
ALA A:153 , LEU A:191 , HOH A:839 , HOH A:964 , ALA B:118 , ARG B:121
BINDING SITE FOR RESIDUE EDO A 804
11
BC2
SOFTWARE
LEU A:117 , ALA A:118 , ARG A:121 , HOH A:848 , HOH A:970 , ALA B:153 , LEU B:191
BINDING SITE FOR RESIDUE EDO A 805
12
BC3
SOFTWARE
TRP B:131 , GLY B:193 , PRO B:195 , ASN B:341 , LEU B:342 , NA B:805 , HOH B:869 , HOH B:989
BINDING SITE FOR RESIDUE EDO B 807
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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)
Info
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1onwa1 (A:1-62,A:347-389)
1b: SCOP_d1onwb1 (B:1-62,B:347-389)
2a: SCOP_d1onwa2 (A:63-346)
2b: SCOP_d1onwb2 (B:63-346)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Composite domain of metallo-dependent hydrolases
(103)
Superfamily
:
Composite domain of metallo-dependent hydrolases
(103)
Family
:
Isoaspartyl dipeptidase
(5)
Protein domain
:
Isoaspartyl dipeptidase
(5)
Escherichia coli [TaxId: 562]
(5)
1a
d1onwa1
A:1-62,A:347-389
1b
d1onwb1
B:1-62,B:347-389
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Isoaspartyl dipeptidase, catalytic domain
(5)
Protein domain
:
Isoaspartyl dipeptidase, catalytic domain
(5)
Escherichia coli [TaxId: 562]
(5)
2a
d1onwa2
A:63-346
2b
d1onwb2
B:63-346
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1onwB02 (B:64-342)
1b: CATH_1onwA02 (A:64-342)
2a: CATH_1onwA01 (A:1-63,A:343-389)
2b: CATH_1onwB01 (B:1-63,B:343-389)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Escherichia coli. Organism_taxid: 562.
(27)
1a
1onwB02
B:64-342
1b
1onwA02
A:64-342
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Urease, subunit C; domain 1
(95)
Homologous Superfamily
:
Urease, subunit C, domain 1
(95)
Escherichia coli. Organism_taxid: 562.
(12)
2a
1onwA01
A:1-63,A:343-389
2b
1onwB01
B:1-63,B:343-389
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Amidohydro_5_1onwB01 (B:28-100)
1b: PFAM_Amidohydro_5_1onwB02 (B:28-100)
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)
Clan
:
Amidohydrolase
(126)
Family
:
Amidohydro_5
(8)
Escherichia coli (strain K12)
(6)
1a
Amidohydro_5-1onwB01
B:28-100
1b
Amidohydro_5-1onwB02
B:28-100
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Asymmetric Unit 1
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