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2OW6
Asym. Unit
Info
Asym.Unit (412 KB)
Biol.Unit 1 (406 KB)
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(1)
Title
:
GOLGI ALPHA-MANNOSIDASE II COMPLEX WITH (1R,5S,6S,7R,8S)-1-THIONIABICYCLO[4.3.0]NONAN-5,7,8-TRIOL CHLORIDE
Authors
:
D. A. Kuntz
Date
:
15 Feb 07 (Deposition) - 08 Jan 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.19
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Glycosyl Hydrolase Family 38, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. S. Kumar, D. A. Kuntz, X. Wen, B. M. Pinto, D. R. Rose
Binding Of Sulfonium-Ion Analogues Of Di-Epi-Swainsonine An 8-Epi-Lentiginosine To Drosophila Golgi Alpha-Mannosidase Ii: The Role Of Water In Inhibitor Binding.
Proteins V. 71 1484 2008
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Hetero Components
(5, 6)
Info
All Hetero Components
1a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3a: (1R,5S,6S,7R,8S)-1-THIONIABICYCLO[... (NK1a)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
5a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MRD
1
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
2
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
NK1
1
Ligand/Ion
(1R,5S,6S,7R,8S)-1-THIONIABICYCLO[4.3.0]NONAN-5,7,8-TRIOL
4
PO4
2
Ligand/Ion
PHOSPHATE ION
5
ZN
1
Ligand/Ion
ZINC ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:194
BINDING SITE FOR RESIDUE NAG A 2001
2
AC2
SOFTWARE
ARG A:770 , ARG A:893 , SER A:924 , HOH A:5103 , HOH A:5104 , HOH A:5382 , HOH A:5387 , HOH A:5388 , HOH A:6097 , HOH A:6437
BINDING SITE FOR RESIDUE PO4 A 2002
3
AC3
SOFTWARE
SER A:112 , PHE A:137 , HOH A:5871 , HOH A:5872
BINDING SITE FOR RESIDUE PO4 A 2003
4
AC4
SOFTWARE
HIS A:90 , ASP A:92 , ASP A:204 , HIS A:471 , NK1 A:4001
BINDING SITE FOR RESIDUE ZN A 3001
5
AC5
SOFTWARE
ASP A:92 , TRP A:95 , ASP A:204 , PHE A:206 , ARG A:228 , TYR A:269 , ASP A:341 , TRP A:415 , HIS A:471 , ASP A:472 , TYR A:727 , ARG A:876 , ZN A:3001
BINDING SITE FOR RESIDUE NK1 A 4001
6
AC6
SOFTWARE
LYS A:63 , GLN A:64 , TYR A:267 , HIS A:273 , HOH A:5643 , HOH A:5645 , HOH A:5646 , HOH A:5691
BINDING SITE FOR RESIDUE MRD A 5001
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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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
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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, 3)
Info
All SCOP Domains
1a: SCOP_d2ow6a1 (A:412-522)
2a: SCOP_d2ow6a2 (A:523-1045)
3a: SCOP_d2ow6a3 (A:30-411)
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Classes
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Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
immunoglobulin/albumin-binding domain-like
(130)
Superfamily
:
Families 57/38 glycoside transferase middle domain
(64)
Family
:
alpha-mannosidase, domain 2
(58)
Protein domain
:
Golgi alpha-mannosidase II
(57)
Fruit fly (Drosophila melanogaster) [TaxId: 7227]
(57)
1a
d2ow6a1
A:412-522
Class
:
All beta proteins
(24004)
Fold
:
Supersandwich
(271)
Superfamily
:
Galactose mutarotase-like
(205)
Family
:
alpha-mannosidase, C-terminal domain
(58)
Protein domain
:
Golgi alpha-mannosidase II
(57)
Fruit fly (Drosophila melanogaster) [TaxId: 7227]
(57)
2a
d2ow6a2
A:523-1045
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
7-stranded beta/alpha barrel
(137)
Superfamily
:
Glycoside hydrolase/deacetylase
(89)
Family
:
alpha-mannosidase
(58)
Protein domain
:
Golgi alpha-mannosidase II
(57)
Fruit fly (Drosophila melanogaster) [TaxId: 7227]
(57)
3a
d2ow6a3
A:30-411
[
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]
CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_2ow6A01 (A:30-411)
2a: CATH_2ow6A02 (A:412-522)
3a: CATH_2ow6A04 (A:648-927)
4a: CATH_2ow6A05 (A:950-1045)
5a: CATH_2ow6A03 (A:523-647,A:928-949)
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)
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Topologies
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)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
7-stranded beta/alpha barrel
(59)
Homologous Superfamily
:
Glycoside hydrolase 38, N terminal domain
(59)
Fruit fly (Drosophila melanogaster)
(57)
1a
2ow6A01
A:30-411
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Substrate Binding Domain Of Dnak; Chain:A; Domain 2
(103)
Homologous Superfamily
:
Families 57/38 glycoside transferase; middle domain
(57)
Fruit fly (Drosophila melanogaster)
(57)
2a
2ow6A02
A:412-522
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
Golgi alpha-mannosidase II; domain 4
(58)
Fruit fly (Drosophila melanogaster)
(57)
3a
2ow6A04
A:648-927
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.1360, no name defined]
(58)
Fruit fly (Drosophila melanogaster)
(57)
4a
2ow6A05
A:950-1045
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Fruit fly (Drosophila melanogaster)
(57)
5a
2ow6A03
A:523-647,A:928-949
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_38_2ow6A01 (A:82-408)
2a: PFAM_Glyco_hydro_38C_2ow6A02 (A:553-1040)
3a: PFAM_Alpha_mann_mid_2ow6A03 (A:413-490)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GH_CE
(28)
Family
:
Glyco_hydro_38
(17)
Drosophila melanogaster (Fruit fly)
(13)
1a
Glyco_hydro_38-2ow6A01
A:82-408
Clan
:
Gal_mutarotase
(81)
Family
:
Glyco_hydro_38C
(17)
Drosophila melanogaster (Fruit fly)
(13)
2a
Glyco_hydro_38C-2ow6A02
A:553-1040
Clan
:
no clan defined [family: Alpha-mann_mid]
(17)
Family
:
Alpha-mann_mid
(17)
Drosophila melanogaster (Fruit fly)
(13)
3a
Alpha-mann_mid-2ow6A03
A:413-490
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Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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Asym.Unit (412 KB)
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