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1IWB
Asym. Unit
Info
Asym.Unit (303 KB)
Biol.Unit 1 (294 KB)
Biol.Unit 2 (294 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIOL DEHYDRATASE
Authors
:
N. Shibata, J. Masuda, Y. Morimoto, N. Yasuoka, T. Toraya
Date
:
01 May 02 (Deposition) - 01 May 03 (Release) - 24 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,E,G,L,M
Biol. Unit 1: A,B,E,G,L,M (1x)
Biol. Unit 2: A,B,E,G,L,M (1x)
Keywords
:
Beta-Alpha-Barrels, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Shibata, J. Masuda, Y. Morimoto, N. Yasuoka, T. Toraya
Substrate-Induced Conformational Change Of A Coenzyme B12-Dependent Enzyme: Crystal Structure Of The Substrate-Free Form Of Diol Dehydratase
Biochemistry V. 41 12607 2002
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: COBALAMIN (B12a)
1b: COBALAMIN (B12b)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
2e: POTASSIUM ION (Ke)
2f: POTASSIUM ION (Kf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B12
2
Ligand/Ion
COBALAMIN
2
K
6
Ligand/Ion
POTASSIUM 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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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:141 , GLU A:170 , GLU A:221 , GLN A:296 , SER A:362 , HOH A:2605 , HOH A:2606
BINDING SITE FOR RESIDUE K A 2602
2
AC2
SOFTWARE
GLY A:261 , SER A:264 , GLU A:265 , GLU A:280 , CYS A:283 , HOH A:2682
BINDING SITE FOR RESIDUE K A 2603
3
AC3
SOFTWARE
LEU A:203 , GLU A:205 , GLU A:208 , THR A:222 , B12 B:1601
BINDING SITE FOR RESIDUE K A 2604
4
AC4
SOFTWARE
GLN L:141 , GLU L:170 , GLU L:221 , GLN L:296 , SER L:362 , HOH L:3605 , HOH L:3606
BINDING SITE FOR RESIDUE K L 3602
5
AC5
SOFTWARE
GLY L:261 , SER L:264 , GLU L:265 , GLU L:280 , CYS L:283 , HOH L:3609 , HOH L:3676
BINDING SITE FOR RESIDUE K L 3603
6
AC6
SOFTWARE
B12 E:1602 , LEU L:203 , GLU L:205 , GLU L:208 , THR L:222
BINDING SITE FOR RESIDUE K L 3604
7
AC7
SOFTWARE
THR A:172 , GLU A:205 , THR A:222 , SER A:224 , ASP A:234 , GLN A:267 , MET A:268 , GLN A:336 , MET A:373 , PHE A:374 , K A:2604 , HOH A:2622 , HOH A:2626 , 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 , ARG B:193 , TYR B:196 , SER B:200 , HOH B:1603 , HOH B:1605 , HOH B:1617 , HOH B:1618 , HOH B:1645
BINDING SITE FOR RESIDUE B12 B 1601
8
AC8
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:1604 , HOH E:1608 , HOH E:1612 , HOH E:1613 , HOH E:1622 , HOH E:1623 , HOH E:1625 , HOH E:1641 , HOH E:1643 , THR L:172 , VAL L:173 , SER L:202 , GLU L:205 , THR L:222 , SER L:224 , ASP L:234 , GLN L:267 , MET L:268 , GLN L:336 , MET L:373 , PHE L:374 , K L:3604 , HOH L:3788
BINDING SITE FOR RESIDUE B12 E 1602
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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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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1iwbg_ (G:)
1b: SCOP_d1iwbm_ (M:)
2a: SCOP_d1iwbb_ (B:)
2b: SCOP_d1iwbe_ (E:)
3a: SCOP_d1iwba_ (A:)
3b: SCOP_d1iwbl_ (L:)
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(
)
Protein Domains
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)
(
)
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
d1iwbg_
G:
1b
d1iwbm_
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
d1iwbb_
B:
2b
d1iwbe_
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
d1iwba_
A:
3b
d1iwbl_
L:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1iwbE00 (E:46-222)
1b: CATH_1iwbB00 (B:46-223)
2a: CATH_1iwbA00 (A:1-551)
2b: CATH_1iwbL00 (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
1iwbE00
E:46-222
1b
1iwbB00
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
1iwbA00
A:1-551
2b
1iwbL00
L:1-551
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Pfam Domains
(0, 0)
Info
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (303 KB)
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