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1UC5
Asym. Unit
Info
Asym.Unit (295 KB)
Biol.Unit 1 (288 KB)
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(1)
Title
:
STRUCTURE OF DIOL DEHYDRATASE COMPLEXED WITH (R)-1,2-PROPANEDIOL
Authors
:
N. Shibata, Y. Nakanishi, M. Fukuoka, M. Yamanishi, N. Yasuoka, T. Toraya
Date
:
08 Apr 03 (Deposition) - 22 Jul 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,E,G,L,M
Biol. Unit 1: A,B,E,G,L,M (1x)
Keywords
:
Alpha/Beta Barrel, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Shibata, Y. Nakanishi, M. Fukuoka, M. Yamanishi, N. Yasuoka, T. Toraya
Structural Rationalization For The Lack Of Stereospecificity In Coenzyme B12-Dependent Diol Dehydratase
J. Biol. Chem. V. 278 22717 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: CO-CYANOCOBALAMIN (CNCa)
1b: CO-CYANOCOBALAMIN (CNCb)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
3a: AMMONIUM ION (NH4a)
3b: AMMONIUM ION (NH4b)
3c: AMMONIUM ION (NH4c)
3d: AMMONIUM ION (NH4d)
4a: R-1,2-PROPANEDIOL (PGRa)
4b: R-1,2-PROPANEDIOL (PGRb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CNC
2
Ligand/Ion
CO-CYANOCOBALAMIN
2
K
2
Ligand/Ion
POTASSIUM ION
3
NH4
4
Ligand/Ion
AMMONIUM ION
4
PGR
2
Ligand/Ion
R-1,2-PROPANEDIOL
[
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]
Sites
(10, 10)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:141 , GLU A:170 , GLU A:221 , GLN A:296 , SER A:362 , PGR A:1602
BINDING SITE FOR RESIDUE K A 1603
02
AC2
SOFTWARE
GLY A:261 , SER A:264 , GLU A:265 , GLU A:280 , CYS A:283 , HOH A:1637
BINDING SITE FOR RESIDUE NH4 A 1604
03
AC3
SOFTWARE
LEU A:203 , GLU A:205 , GLU A:208 , THR A:222 , CNC B:1601
BINDING SITE FOR RESIDUE NH4 A 1605
04
AC4
SOFTWARE
GLN L:141 , GLU L:170 , GLU L:221 , GLN L:296 , SER L:362 , PGR L:2602
BINDING SITE FOR RESIDUE K L 2603
05
AC5
SOFTWARE
GLY L:261 , SER L:264 , GLU L:265 , GLU L:280 , CYS L:283 , HOH L:2606 , HOH L:2672
BINDING SITE FOR RESIDUE NH4 L 2604
06
AC6
SOFTWARE
CNC E:2601 , LEU L:203 , GLU L:205 , GLU L:208 , THR L:222
BINDING SITE FOR RESIDUE NH4 L 2605
07
AC7
SOFTWARE
THR A:172 , SER A:202 , GLU A:205 , THR A:222 , SER A:224 , ASP A:234 , GLN A:267 , MET A:268 , SER A:301 , GLN A:336 , MET A:373 , PHE A:374 , NH4 A:1605 , HOH A:1609 , ASP B:112 , VAL B:113 , LYS B:135 , THR B:137 , LEU B:148 , ASN B:150 , LEU B:153 , PRO B:155 , GLN B:156 , ALA B:157 , PRO B:158 , ARG B:193 , TYR B:196 , SER B:200 , HOH B:1607 , HOH B:1608 , HOH B:1619 , HOH B:1620 , HOH B:1624 , HOH B:1652
BINDING SITE FOR RESIDUE CNC B 1601
08
AC8
SOFTWARE
HIS A:143 , GLU A:170 , GLU A:221 , THR A:222 , GLN A:296 , SER A:301 , ASP A:335 , GLN A:336 , SER A:362 , PHE A:374 , K A:1603
BINDING SITE FOR RESIDUE PGR A 1602
09
AC9
SOFTWARE
ASP E:112 , VAL E:113 , LYS E:135 , THR E:137 , LEU E:148 , ASN E:150 , LEU E:153 , PRO E:155 , GLN E:156 , ALA E:157 , PRO E:158 , ARG E:193 , TYR E:196 , SER E:200 , HOH E:2603 , HOH E:2609 , HOH E:2616 , HOH E:2619 , THR L:172 , VAL L:173 , ALA L:174 , SER L:202 , GLU L:205 , THR L:222 , SER L:224 , ASP L:234 , GLN L:267 , MET L:268 , SER L:301 , GLN L:336 , MET L:373 , PHE L:374 , NH4 L:2605 , HOH L:2648
BINDING SITE FOR RESIDUE CNC E 2601
10
BC1
SOFTWARE
HIS L:143 , GLU L:170 , GLU L:221 , THR L:222 , GLN L:296 , SER L:301 , ASP L:335 , GLN L:336 , SER L:362 , PHE L:374 , K L:2603
BINDING SITE FOR RESIDUE PGR L 2602
[
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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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;
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Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1uc5g_ (G:)
1b: SCOP_d1uc5m_ (M:)
2a: SCOP_d1uc5b_ (B:)
2b: SCOP_d1uc5e_ (E:)
3a: SCOP_d1uc5a_ (A:)
3b: SCOP_d1uc5l_ (L:)
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(
)
(
)
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(
)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Open three-helical up-and-down bundle
(49)
Superfamily
:
Diol dehydratase, gamma subunit
(10)
Family
:
Diol dehydratase, gamma subunit
(10)
Protein domain
:
Diol dehydratase, gamma subunit
(10)
Klebsiella oxytoca [TaxId: 571]
(8)
1a
d1uc5g_
G:
1b
d1uc5m_
M:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Anticodon-binding domain-like
(97)
Superfamily
:
B12-dependent dehydatase associated subunit
(14)
Family
:
Diol dehydratase, beta subunit
(10)
Protein domain
:
Diol dehydratase, beta subunit
(10)
Klebsiella oxytoca [TaxId: 571]
(8)
2a
d1uc5b_
B:
2b
d1uc5e_
E:
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Cobalamin (vitamin B12)-dependent enzymes
(30)
Family
:
Diol dehydratase, alpha subunit
(10)
Protein domain
:
Diol dehydratase, alpha subunit
(9)
Klebsiella oxytoca [TaxId: 571]
(7)
3a
d1uc5a_
A:
3b
d1uc5l_
L:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1uc5E00 (E:46-222)
1b: CATH_1uc5B00 (B:46-223)
2a: CATH_1uc5A00 (A:1-551)
2b: CATH_1uc5L00 (L:1-551)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Diol Dehydratase; Chain B
(11)
Klebsiella oxytoca. Organism_taxid: 571.
(4)
1a
1uc5E00
E:46-222
1b
1uc5B00
B:46-223
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
[code=3.20.20.350, no name defined]
(9)
Klebsiella oxytoca. Organism_taxid: 571.
(4)
2a
1uc5A00
A:1-551
2b
1uc5L00
L:1-551
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Dehydratase_LU_1uc5L01 (L:1-551)
1b: PFAM_Dehydratase_LU_1uc5L02 (L:1-551)
2a: PFAM_Dehydratase_MU_1uc5E01 (E:67-185)
2b: PFAM_Dehydratase_MU_1uc5E02 (E:67-185)
3a: PFAM_Dehydratase_SU_1uc5M01 (M:37-170)
3b: PFAM_Dehydratase_SU_1uc5M02 (M:37-170)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Dehydratase_LU]
(2)
Family
:
Dehydratase_LU
(2)
Klebsiella oxytoca
(1)
1a
Dehydratase_LU-1uc5L01
L:1-551
1b
Dehydratase_LU-1uc5L02
L:1-551
Clan
:
no clan defined [family: Dehydratase_MU]
(3)
Family
:
Dehydratase_MU
(3)
Klebsiella oxytoca
(1)
2a
Dehydratase_MU-1uc5E01
E:67-185
2b
Dehydratase_MU-1uc5E02
E:67-185
Clan
:
no clan defined [family: Dehydratase_SU]
(2)
Family
:
Dehydratase_SU
(2)
Klebsiella oxytoca
(1)
3a
Dehydratase_SU-1uc5M01
M:37-170
3b
Dehydratase_SU-1uc5M02
M:37-170
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