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.
2WW0
Asym. Unit
Info
Asym.Unit (964 KB)
Biol.Unit 1 (133 KB)
Biol.Unit 2 (133 KB)
Biol.Unit 3 (132 KB)
Biol.Unit 4 (132 KB)
Biol.Unit 5 (131 KB)
Biol.Unit 6 (130 KB)
Biol.Unit 7 (128 KB)
Biol.Unit 8 (128 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
Authors
:
M. D. L. Suits, A. Thompson, Y. Zhu, H. J. Gilbert, G. J. Davies
Date
:
21 Oct 09 (Deposition) - 29 Dec 09 (Release) - 22 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
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
:
Hydrolase, Gh92, Bt3990, Glycoside Hydrolase Family 92
(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
(3, 33)
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)
3a: 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2... (SWAa)
3b: 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2... (SWAb)
3c: 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2... (SWAc)
3d: 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2... (SWAd)
3e: 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2... (SWAe)
3f: 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2... (SWAf)
3g: 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2... (SWAg)
3h: 1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2... (SWAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
8
Ligand/Ion
CALCIUM ION
2
GOL
17
Ligand/Ion
GLYCEROL
3
SWA
8
Ligand/Ion
1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL
[
close Hetero Component info
]
Sites
(33, 33)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:601 , GLN A:602 , ASP A:644 , SWA A:801 , HOH A:2097
BINDING SITE FOR RESIDUE CA A 800
02
AC2
SOFTWARE
SER A:86 , TRP A:347 , ASP A:348 , TRP A:385 , MET A:394 , GLU A:533 , GLU A:585 , ASN A:601 , GLN A:602 , ASP A:644 , CA A:800
BINDING SITE FOR RESIDUE SWA A 801
03
AC3
SOFTWARE
TYR A:126 , GLU A:272
BINDING SITE FOR RESIDUE GOL A 802
04
AC4
SOFTWARE
GLY A:293 , GLN A:298 , ARG A:625 , ASP A:629 , LEU A:675 , SER A:697
BINDING SITE FOR RESIDUE GOL A 803
05
AC5
SOFTWARE
PRO A:330 , TYR A:331 , HIS A:390 , HOH A:2117
BINDING SITE FOR RESIDUE GOL A 804
06
AC6
SOFTWARE
LYS A:315 , TYR A:317 , GLU A:367
BINDING SITE FOR RESIDUE GOL A 805
07
AC7
SOFTWARE
LYS A:619 , TYR A:702
BINDING SITE FOR RESIDUE GOL A 806
08
AC8
SOFTWARE
ASN B:601 , GLN B:602 , ASP B:644 , SWA B:801 , HOH B:2096
BINDING SITE FOR RESIDUE CA B 800
09
AC9
SOFTWARE
TRP B:88 , TRP B:347 , ASP B:348 , TRP B:385 , MET B:394 , GLU B:533 , ASN B:601 , GLN B:602 , ASP B:644 , CA B:800 , HOH B:2096
BINDING SITE FOR RESIDUE SWA B 801
10
BC1
SOFTWARE
GLN B:284 , LYS B:288 , VAL B:364 , GLU B:684
BINDING SITE FOR RESIDUE GOL B 802
11
BC2
SOFTWARE
ALA B:275 , HOH B:2039 , HOH B:2041
BINDING SITE FOR RESIDUE GOL B 803
12
BC3
SOFTWARE
LYS B:315 , TYR B:317 , GLU B:367
BINDING SITE FOR RESIDUE GOL B 804
13
BC4
SOFTWARE
ASN C:601 , GLN C:602 , ASP C:644 , SWA C:801 , HOH C:2061
BINDING SITE FOR RESIDUE CA C 800
14
BC5
SOFTWARE
TRP C:88 , TRP C:347 , ASP C:348 , TRP C:385 , MET C:394 , GLU C:533 , ASN C:601 , GLN C:602 , ASP C:644 , CA C:800 , HOH C:2061
BINDING SITE FOR RESIDUE SWA C 801
15
BC6
SOFTWARE
TYR C:702
BINDING SITE FOR RESIDUE GOL C 802
16
BC7
SOFTWARE
ASN C:195 , LYS C:197 , TYR C:199 , PHE C:253 , ILE C:254 , TYR C:328
BINDING SITE FOR RESIDUE GOL C 803
17
BC8
SOFTWARE
GLN C:284 , LYS C:288 , TYR C:361 , GLU C:684
BINDING SITE FOR RESIDUE GOL C 804
18
BC9
SOFTWARE
ASN D:601 , GLN D:602 , ASP D:644 , SWA D:801 , HOH D:2094
BINDING SITE FOR RESIDUE CA D 800
19
CC1
SOFTWARE
TRP D:88 , TRP D:347 , ASP D:348 , TRP D:385 , MET D:394 , GLU D:533 , ASN D:601 , GLN D:602 , ASP D:644 , CA D:800 , HOH D:2094
BINDING SITE FOR RESIDUE SWA D 801
20
CC2
SOFTWARE
TYR D:126 , GLU D:272
BINDING SITE FOR RESIDUE GOL D 802
21
CC3
SOFTWARE
ASN D:709 , LYS D:725 , GLY D:727 , HOH D:2105
BINDING SITE FOR RESIDUE GOL D 803
22
CC4
SOFTWARE
GLN D:284 , LYS D:288 , SER D:363 , GLU D:684
BINDING SITE FOR RESIDUE GOL D 804
23
CC5
SOFTWARE
ASN E:601 , GLN E:602 , ASP E:644 , SWA E:801
BINDING SITE FOR RESIDUE CA E 800
24
CC6
SOFTWARE
TRP E:347 , ASP E:348 , TRP E:385 , MET E:394 , GLU E:533 , ASN E:601 , GLN E:602 , ASP E:644 , CA E:800
BINDING SITE FOR RESIDUE SWA E 801
25
CC7
SOFTWARE
GLY B:580 , ASN E:195 , TYR E:199 , ILE E:254 , VAL E:335
BINDING SITE FOR RESIDUE GOL E 802
26
CC8
SOFTWARE
TYR E:126
BINDING SITE FOR RESIDUE GOL E 803
27
CC9
SOFTWARE
ASN F:601 , GLN F:602 , ASP F:644 , SWA F:801
BINDING SITE FOR RESIDUE CA F 800
28
DC1
SOFTWARE
TRP F:347 , ASP F:348 , TRP F:385 , GLU F:533 , GLU F:585 , ASN F:601 , GLN F:602 , ASP F:644 , CA F:800
BINDING SITE FOR RESIDUE SWA F 801
29
DC2
SOFTWARE
TYR F:126 , GLU F:272
BINDING SITE FOR RESIDUE GOL F 802
30
DC3
SOFTWARE
ASN G:601 , GLN G:602 , ASP G:644 , SWA G:801
BINDING SITE FOR RESIDUE CA G 800
31
DC4
SOFTWARE
TRP G:88 , TRP G:347 , ASP G:348 , TRP G:385 , MET G:394 , GLU G:533 , GLU G:585 , ASN G:601 , GLN G:602 , ASP G:642 , ASP G:644 , CA G:800
BINDING SITE FOR RESIDUE SWA G 801
32
DC5
SOFTWARE
ASN H:601 , GLN H:602 , ASP H:644 , SWA H:801
BINDING SITE FOR RESIDUE CA H 800
33
DC6
SOFTWARE
TRP H:347 , ASP H:348 , TRP H:385 , GLU H:533 , GLU H:585 , ASN H:601 , GLN H:602 , ASP H:644 , CA H:800
BINDING SITE FOR RESIDUE SWA H 801
[
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
(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_2ww0A02 (A:289-312,A:607-631,A:632-748)
1b: CATH_2ww0B02 (B:289-312,B:607-631,B:632-748)
1c: CATH_2ww0C02 (C:289-312,C:607-631,C:632-748)
1d: CATH_2ww0D02 (D:289-312,D:607-631,D:632-748)
1e: CATH_2ww0E02 (E:289-312,E:607-631,E:632-748)
1f: CATH_2ww0F02 (F:289-312,F:607-631,F:632-748)
1g: CATH_2ww0G02 (G:289-312,G:607-631,G:632-748)
1h: CATH_2ww0H02 (H:289-312,H:607-631,H:632-748)
2a: CATH_2ww0A03 (A:344-438)
2b: CATH_2ww0B03 (B:344-438)
2c: CATH_2ww0C03 (C:344-438)
2d: CATH_2ww0D03 (D:344-438)
2e: CATH_2ww0E03 (E:344-438)
2f: CATH_2ww0F03 (F:344-438)
2g: CATH_2ww0G03 (G:344-438)
2h: CATH_2ww0H03 (H:344-438)
3a: CATH_2ww0A01 (A:20-53,A:54-288,A:313-343)
3b: CATH_2ww0B01 (B:20-53,B:54-288,B:313-343)
3c: CATH_2ww0C01 (C:20-53,C:54-288,C:313-343)
3d: CATH_2ww0D01 (D:20-53,D:54-288,D:313-343)
3e: CATH_2ww0E01 (E:20-53,E:54-288,E:313-343)
3f: CATH_2ww0F01 (F:20-53,F:54-288,F:313-343)
3g: CATH_2ww0G01 (G:20-53,G:54-288,G:313-343)
3h: CATH_2ww0H01 (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
2ww0A02
A:289-312,A:607-631,A:632-748
1b
2ww0B02
B:289-312,B:607-631,B:632-748
1c
2ww0C02
C:289-312,C:607-631,C:632-748
1d
2ww0D02
D:289-312,D:607-631,D:632-748
1e
2ww0E02
E:289-312,E:607-631,E:632-748
1f
2ww0F02
F:289-312,F:607-631,F:632-748
1g
2ww0G02
G:289-312,G:607-631,G:632-748
1h
2ww0H02
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
2ww0A03
A:344-438
2b
2ww0B03
B:344-438
2c
2ww0C03
C:344-438
2d
2ww0D03
D:344-438
2e
2ww0E03
E:344-438
2f
2ww0F03
F:344-438
2g
2ww0G03
G:344-438
2h
2ww0H03
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
2ww0A01
A:20-53,A:54-288,A:313-343
3b
2ww0B01
B:20-53,B:54-288,B:313-343
3c
2ww0C01
C:20-53,C:54-288,C:313-343
3d
2ww0D01
D:20-53,D:54-288,D:313-343
3e
2ww0E01
E:20-53,E:54-288,E:313-343
3f
2ww0F01
F:20-53,F:54-288,F:313-343
3g
2ww0G01
G:20-53,G:54-288,G:313-343
3h
2ww0H01
H:20-53,H:54-288,H:313-343
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_92_2ww0H01 (H:228-737)
1b: PFAM_Glyco_hydro_92_2ww0H02 (H:228-737)
1c: PFAM_Glyco_hydro_92_2ww0H03 (H:228-737)
1d: PFAM_Glyco_hydro_92_2ww0H04 (H:228-737)
1e: PFAM_Glyco_hydro_92_2ww0H05 (H:228-737)
1f: PFAM_Glyco_hydro_92_2ww0H06 (H:228-737)
1g: PFAM_Glyco_hydro_92_2ww0H07 (H:228-737)
1h: PFAM_Glyco_hydro_92_2ww0H08 (H:228-737)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Pec_lyase
(42)
Family
:
Glyco_hydro_92
(7)
Bacteroides thetaiotaomicron
(7)
1a
Glyco_hydro_92-2ww0H01
H:228-737
1b
Glyco_hydro_92-2ww0H02
H:228-737
1c
Glyco_hydro_92-2ww0H03
H:228-737
1d
Glyco_hydro_92-2ww0H04
H:228-737
1e
Glyco_hydro_92-2ww0H05
H:228-737
1f
Glyco_hydro_92-2ww0H06
H:228-737
1g
Glyco_hydro_92-2ww0H07
H:228-737
1h
Glyco_hydro_92-2ww0H08
H:228-737
[
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
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
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 (964 KB)
Header - Asym.Unit
Biol.Unit 1 (133 KB)
Header - Biol.Unit 1
Biol.Unit 2 (133 KB)
Header - Biol.Unit 2
Biol.Unit 3 (132 KB)
Header - Biol.Unit 3
Biol.Unit 4 (132 KB)
Header - Biol.Unit 4
Biol.Unit 5 (131 KB)
Header - Biol.Unit 5
Biol.Unit 6 (130 KB)
Header - Biol.Unit 6
Biol.Unit 7 (128 KB)
Header - Biol.Unit 7
Biol.Unit 8 (128 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
2WW0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help