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.
2WZS
Biol. Unit 3
Info
Asym.Unit (996 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (138 KB)
Biol.Unit 3 (137 KB)
Biol.Unit 4 (139 KB)
Biol.Unit 5 (135 KB)
Biol.Unit 6 (134 KB)
Biol.Unit 7 (131 KB)
Biol.Unit 8 (132 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE FAMILY GH92 INVERTING MANNOSIDASE BT3990 FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 IN COMPLEX WITH MANNOIMIDAZOLE
Authors
:
Y. Zhu, M. D. L. Suits, A. Thompson, S. Chavan, Z. Dinev, C. Dumon, N. Smith, K. W. Moremen, Y. Xiang, A. Siriwardena, S. J. Williams, H. J. Gilbert, G. J. Davies
Date
:
02 Dec 09 (Deposition) - 29 Dec 09 (Release) - 26 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Keywords
:
Glycoside Hydrolase Family 92, Alpha-1, 2 Linkage, Bt3990, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhu, M. D. L. Suits, A. Thompson, S. Chavan, Z. Dinev, C. Dumon, N. Smith, K. W. Moremen, Y. Xiang, A. Siriwardena, S. J. Williams, H. J. Gilbert, G. J. Davies
Mechanistic Insights Into A Ca2+-Dependent Family Of A-Mannosidases In A Human Gut Symbiont.
Nat. Chem. Biol. V. 6 125 2010
[
close entry info
]
Hetero Components
(2, 5)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
3a: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLa)
3b: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLb)
3c: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLc)
3d: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLd)
3e: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLe)
3f: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLf)
3g: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLg)
3h: (5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(... (MVLh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
4
Ligand/Ion
GLYCEROL
3
MVL
1
Ligand/Ion
(5R,6R,7S,8R)-6,7,8-TRIHYDROXY-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDRO-1H-IMIDAZO[1,2-A]PYRIDIN-4-IUM
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: BC3 (SOFTWARE)
2: BC4 (SOFTWARE)
3: BC5 (SOFTWARE)
4: BC6 (SOFTWARE)
5: BC7 (SOFTWARE)
6: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
BC3
SOFTWARE
ASN C:601 , GLN C:602 , ASP C:644 , MVL C:801 , HOH C:2210 , HOH C:2278 , HOH C:2279
BINDING SITE FOR RESIDUE CA C 800
2
BC4
SOFTWARE
SER C:86 , TRP C:88 , TRP C:347 , ASP C:348 , TRP C:385 , GLU C:533 , GLU C:585 , ASN C:601 , GLN C:602 , ASP C:644 , CA C:800 , HOH C:2232 , HOH C:2278 , HOH C:2279
BINDING SITE FOR RESIDUE MVL C 801
3
BC5
SOFTWARE
GLN C:284 , LYS C:288 , VAL C:364 , GLU C:684
BINDING SITE FOR RESIDUE GOL C 802
4
BC6
SOFTWARE
LYS C:619 , TYR C:622 , TYR C:702
BINDING SITE FOR RESIDUE GOL C 803
5
BC7
SOFTWARE
TRP C:88 , CYS C:393
BINDING SITE FOR RESIDUE GOL C 804
6
BC8
SOFTWARE
GLU C:272
BINDING SITE FOR RESIDUE GOL C 805
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_2wzsA02 (A:289-312,A:607-631,A:632-748)
1b: CATH_2wzsB02 (B:289-312,B:607-631,B:632-748)
1c: CATH_2wzsC02 (C:289-312,C:607-631,C:632-748)
1d: CATH_2wzsD02 (D:289-312,D:607-631,D:632-748)
1e: CATH_2wzsE02 (E:289-312,E:607-631,E:632-748)
1f: CATH_2wzsF02 (F:289-312,F:607-631,F:632-748)
1g: CATH_2wzsG02 (G:289-312,G:607-631,G:632-748)
1h: CATH_2wzsH02 (H:289-312,H:607-631,H:632-748)
2a: CATH_2wzsA03 (A:344-438)
2b: CATH_2wzsB03 (B:344-438)
2c: CATH_2wzsC03 (C:344-438)
2d: CATH_2wzsD03 (D:344-438)
2e: CATH_2wzsE03 (E:344-438)
2f: CATH_2wzsF03 (F:344-438)
2g: CATH_2wzsG03 (G:344-438)
2h: CATH_2wzsH03 (H:344-438)
3a: CATH_2wzsA01 (A:20-53,A:54-288,A:313-343)
3b: CATH_2wzsB01 (B:20-53,B:54-288,B:313-343)
3c: CATH_2wzsC01 (C:20-53,C:54-288,C:313-343)
3d: CATH_2wzsD01 (D:20-53,D:54-288,D:313-343)
3e: CATH_2wzsE01 (E:20-53,E:54-288,E:313-343)
3f: CATH_2wzsF01 (F:20-53,F:54-288,F:313-343)
3g: CATH_2wzsG01 (G:20-53,G:54-288,G:313-343)
3h: CATH_2wzsH01 (H:20-53,H:54-288,H:313-343)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
GH92 mannosidase fold
(8)
Homologous Superfamily
:
GH92 mannosidase domain
(8)
Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482.
(8)
1a
2wzsA02
A:289-312,A:607-631,A:632-748
1b
2wzsB02
B:289-312,B:607-631,B:632-748
1c
2wzsC02
C:289-312,C:607-631,C:632-748
1d
2wzsD02
D:289-312,D:607-631,D:632-748
1e
2wzsE02
E:289-312,E:607-631,E:632-748
1f
2wzsF02
F:289-312,F:607-631,F:632-748
1g
2wzsG02
G:289-312,G:607-631,G:632-748
1h
2wzsH02
H:289-312,H:607-631,H:632-748
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
(267)
Homologous Superfamily
:
alpha-1,2-mannosidase
(8)
Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482.
(8)
2a
2wzsA03
A:344-438
2b
2wzsB03
B:344-438
2c
2wzsC03
C:344-438
2d
2wzsD03
D:344-438
2e
2wzsE03
E:344-438
2f
2wzsF03
F:344-438
2g
2wzsG03
G:344-438
2h
2wzsH03
H:344-438
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Beta-galactosidase; Chain A, domain 5
(250)
Homologous Superfamily
:
[code=2.70.98.10, no name defined]
(116)
Bacteroides thetaiotaomicron. Organism_taxid: 226186. Strain: vpi-5482.
(8)
3a
2wzsA01
A:20-53,A:54-288,A:313-343
3b
2wzsB01
B:20-53,B:54-288,B:313-343
3c
2wzsC01
C:20-53,C:54-288,C:313-343
3d
2wzsD01
D:20-53,D:54-288,D:313-343
3e
2wzsE01
E:20-53,E:54-288,E:313-343
3f
2wzsF01
F:20-53,F:54-288,F:313-343
3g
2wzsG01
G:20-53,G:54-288,G:313-343
3h
2wzsH01
H:20-53,H:54-288,H:313-343
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 C
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 (996 KB)
Header - Asym.Unit
Biol.Unit 1 (138 KB)
Header - Biol.Unit 1
Biol.Unit 2 (138 KB)
Header - Biol.Unit 2
Biol.Unit 3 (137 KB)
Header - Biol.Unit 3
Biol.Unit 4 (139 KB)
Header - Biol.Unit 4
Biol.Unit 5 (135 KB)
Header - Biol.Unit 5
Biol.Unit 6 (134 KB)
Header - Biol.Unit 6
Biol.Unit 7 (131 KB)
Header - Biol.Unit 7
Biol.Unit 8 (132 KB)
Header - Biol.Unit 8
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
2WZS
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help