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1MMF
Asym. Unit
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Asym.Unit (283 KB)
Biol.Unit 1 (140 KB)
Biol.Unit 2 (141 KB)
Biol.Unit 3 (276 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SUBSTRATE FREE FORM OF GLYCEROL DEHYDRATASE
Authors
:
D. I. Liao, G. Dotson, I. Turner, L. Reiss, M. Emptage
Date
:
03 Sep 02 (Deposition) - 10 Jun 03 (Release) - 24 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,E,G,L,M
Biol. Unit 1: A,B,G (1x)
Biol. Unit 2: E,L,M (1x)
Biol. Unit 3: A,B,E,G,L,M (1x)
Keywords
:
Glycerol Dehydratase, Diol Dehydratase, Coenzyme B12, Tim Barrel, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. I. Liao, G. Dotson, I. Turner, L. Reiss, M. Emptage
Crystal Structure Of Substrate Free Form Of Glycerol Dehydratase
J. Inorg. Biochem. V. 93 84 2003
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: COBALAMIN (B12a)
1b: COBALAMIN (B12b)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
B12
2
Ligand/Ion
COBALAMIN
2
K
2
Ligand/Ion
POTASSIUM ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:142 , GLU A:171 , GLU A:222 , GLN A:297 , SER A:363 , HOH A:1006
BINDING SITE FOR RESIDUE K A 1001
2
AC2
SOFTWARE
GLN L:142 , GLU L:171 , GLU L:222 , GLN L:297 , SER L:363 , HOH L:1006
BINDING SITE FOR RESIDUE K L 1002
3
AC3
SOFTWARE
THR A:173 , VAL A:174 , GLY A:175 , SER A:203 , GLU A:206 , THR A:223 , ASP A:235 , LEU A:268 , MET A:269 , GLN A:337 , MET A:374 , PHE A:375 , ASP B:79 , SER B:81 , LYS B:102 , THR B:104 , LEU B:115 , ASN B:117 , LEU B:120 , SER B:122 , GLN B:123 , ALA B:124 , ARG B:160 , PHE B:163 , MET B:164
BINDING SITE FOR RESIDUE B12 B 601
4
AC4
SOFTWARE
ASP E:79 , SER E:81 , LYS E:102 , THR E:104 , VAL E:106 , LEU E:115 , ASN E:117 , LEU E:120 , SER E:122 , GLN E:123 , ALA E:124 , ARG E:160 , PHE E:163 , HOH E:607 , HOH E:610 , THR L:173 , SER L:203 , GLU L:206 , THR L:223 , ASP L:235 , LEU L:268 , MET L:269 , SER L:302 , GLN L:337 , MET L:374 , PHE L:375 , ALA L:376 , HOH L:1050
BINDING SITE FOR RESIDUE B12 E 602
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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_d1mmfg_ (G:)
1b: SCOP_d1mmfm_ (M:)
2a: SCOP_d1mmfb_ (B:)
2b: SCOP_d1mmfe_ (E:)
3a: SCOP_d1mmfa_ (A:)
3b: SCOP_d1mmfl_ (L:)
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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 pneumoniae [TaxId: 573]
(2)
1a
d1mmfg_
G:
1b
d1mmfm_
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 pneumoniae [TaxId: 573]
(2)
2a
d1mmfb_
B:
2b
d1mmfe_
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 pneumoniae [TaxId: 573]
(2)
3a
d1mmfa_
A:
3b
d1mmfl_
L:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1mmfB00 (B:11-191)
1b: CATH_1mmfE00 (E:10-193)
2a: CATH_1mmfA00 (A:1-552)
2b: CATH_1mmfL00 (L:1-555)
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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 pneumoniae. Organism_taxid: 573.
(1)
1a
1mmfB00
B:11-191
1b
1mmfE00
E:10-193
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
[code=3.20.20.350, no name defined]
(9)
Klebsiella pneumoniae. Organism_taxid: 573.
(1)
2a
1mmfA00
A:1-552
2b
1mmfL00
L:1-555
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Dehydratase_LU_1mmfL01 (L:2-555)
1b: PFAM_Dehydratase_LU_1mmfL02 (L:2-555)
2a: PFAM_Dehydratase_MU_1mmfE01 (E:34-153)
2b: PFAM_Dehydratase_MU_1mmfE02 (E:34-153)
3a: PFAM_Dehydratase_SU_1mmfM01 (M:11-138)
3b: PFAM_Dehydratase_SU_1mmfM02 (M:11-138)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Dehydratase_LU]
(2)
Family
:
Dehydratase_LU
(2)
Klebsiella pneumoniae
(1)
1a
Dehydratase_LU-1mmfL01
L:2-555
1b
Dehydratase_LU-1mmfL02
L:2-555
Clan
:
no clan defined [family: Dehydratase_MU]
(3)
Family
:
Dehydratase_MU
(3)
Klebsiella pneumoniae
(2)
2a
Dehydratase_MU-1mmfE01
E:34-153
2b
Dehydratase_MU-1mmfE02
E:34-153
Clan
:
no clan defined [family: Dehydratase_SU]
(2)
Family
:
Dehydratase_SU
(2)
Klebsiella pneumoniae
(1)
3a
Dehydratase_SU-1mmfM01
M:11-138
3b
Dehydratase_SU-1mmfM02
M:11-138
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Asym.Unit (283 KB)
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