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1MMF
Biol. Unit 1
Info
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:
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Gene Ontology, PubMed, Web (Google)
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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
(1, 1)
Info
All Hetero Components
1a: COBALAMIN (B12a)
1b: COBALAMIN (B12b)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
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Label:
No.
Name
Count
Type
Full Name
1
B12
1
Ligand/Ion
COBALAMIN
2
K
-1
Ligand/Ion
POTASSIUM ION
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
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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
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
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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
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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
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(
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Organisms
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(
)
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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)
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(
)
(
)
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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Asymmetric Unit 1
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Asym.Unit (283 KB)
Header - Asym.Unit
Biol.Unit 1 (140 KB)
Header - Biol.Unit 1
Biol.Unit 2 (141 KB)
Header - Biol.Unit 2
Biol.Unit 3 (276 KB)
Header - Biol.Unit 3
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