PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1QWN
Asym. Unit
Info
Asym.Unit (199 KB)
Biol.Unit 1 (193 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
GOLGI ALPHA-MANNOSIDASE II COVALENT INTERMEDIATE COMPLEX WITH 5-FLUORO-GULOSYL-FLUORIDE
Authors
:
S. Numao, D. A. Kuntz, S. G. Withers, D. R. Rose
Date
:
02 Sep 03 (Deposition) - 07 Oct 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
N-Terminal Alpha-Beta Domain, Three Helix Bundle, 2 C-Terminal Beta Barrels, Family 38 Glycosyl Hydrolase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Numao, D. A. Kuntz, S. G. Withers, D. R. Rose
Insights Into The Mechanism Of Drosophila Melanogaster Golg Alpha-Mannosidase Ii Through The Structural Analysis Of Covalent Reaction Intermediates.
J. Biol. Chem. V. 278 48074 2003
[
close entry info
]
Hetero Components
(5, 5)
Info
All Hetero Components
1a: 5-FLUORO-BETA-L-GULOSYL FLUORIDE (GULa)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
5a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GUL
1
Ligand/Ion
5-FLUORO-BETA-L-GULOSYL FLUORIDE
2
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:194
BINDING SITE FOR RESIDUE NAG A 2001
2
AC2
SOFTWARE
HIS A:90 , ASP A:92 , ASP A:204 , HIS A:471 , GUL A:2003
BINDING SITE FOR RESIDUE ZN A 2005
3
AC3
SOFTWARE
HIS A:90 , ASP A:92 , TRP A:95 , ASP A:204 , PHE A:206 , ARG A:228 , TYR A:269 , TRP A:415 , HIS A:471 , ASP A:472 , TYR A:727 , ARG A:876 , TRS A:2004 , ZN A:2005
BINDING SITE FOR RESIDUE GUL A 2003
4
AC4
SOFTWARE
ARG A:228 , TYR A:269 , ASP A:340 , ASP A:341 , GUL A:2003 , HOH A:2752 , HOH A:2880 , HOH A:2882 , HOH A:2887 , HOH A:2889
BINDING SITE FOR RESIDUE TRS A 2004
5
AC5
SOFTWARE
LYS A:63 , GLN A:64 , HIS A:273 , HOH A:2153 , HOH A:2629 , HOH A:2702 , HOH A:2845
BINDING SITE FOR RESIDUE MPD A 2002
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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_d1qwna1 (A:412-522)
2a: SCOP_d1qwna2 (A:523-1044)
3a: SCOP_d1qwna3 (A:31-411)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
d1qwna1
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
d1qwna2
A:523-1044
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
d1qwna3
A:31-411
[
close SCOP info
]
CATH Domains
(5, 5)
Info
all CATH domains
1a: CATH_1qwnA01 (A:31-411)
2a: CATH_1qwnA02 (A:412-522)
3a: CATH_1qwnA04 (A:648-927)
4a: CATH_1qwnA05 (A:950-1044)
5a: CATH_1qwnA03 (A:523-647,A:928-949)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
1qwnA01
A:31-411
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
1qwnA02
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
1qwnA04
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
1qwnA05
A:950-1044
Homologous Superfamily
:
Golgi alpha-mannosidase II
(346)
Fruit fly (Drosophila melanogaster)
(57)
5a
1qwnA03
A:523-647,A:928-949
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_38_1qwnA01 (A:82-408)
2a: PFAM_Glyco_hydro_38C_1qwnA02 (A:553-1040)
3a: PFAM_Alpha_mann_mid_1qwnA03 (A:413-490)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GH_CE
(28)
Family
:
Glyco_hydro_38
(17)
Drosophila melanogaster (Fruit fly)
(13)
1a
Glyco_hydro_38-1qwnA01
A:82-408
Clan
:
Gal_mutarotase
(81)
Family
:
Glyco_hydro_38C
(17)
Drosophila melanogaster (Fruit fly)
(13)
2a
Glyco_hydro_38C-1qwnA02
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-1qwnA03
A:413-490
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (199 KB)
Header - Asym.Unit
Biol.Unit 1 (193 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1QWN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
