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.
3QED
Asym. Unit
Info
Asym.Unit (211 KB)
Biol.Unit 1 (54 KB)
Biol.Unit 2 (55 KB)
Biol.Unit 3 (55 KB)
Biol.Unit 4 (55 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURE AND FUNCTION OF AN ARABINAN-SPECIFIC ALPHA-1,2-ARABINOFURANOSIDASE IDENTIFIED FROM SCREENING THE ACTIVITIES OF BACTERIAL GH43 GLYCOSIDE HYDROLASES
Authors
:
A. Cartmell, L. S. Mckee, M. Pena, J. Larsbrink, H. Brumer, R. J. Lewis, A Nielsen, H. J. Gilbert, J. Marles-Wright
Date
:
20 Jan 11 (Deposition) - 16 Feb 11 (Release) - 11 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.99
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
5-Bladed Beta Propeller, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Cartmell, L. S. Mckee, M. J. Pena, J. Larsbrink, H. Brumer, S. Kaneko H. Ichinose, R. J. Lewis, A. Vikso-Nielsen, H. J. Gilbert, J. Marles-Wright
The Structure And Function Of An Arabinan-Specific {Alpha}-1, 2-Arabinofuranosidase Identified From Screening The Activities Of Bacterial Gh43 Glycoside Hydrolases.
J. Biol. Chem. V. 286 15483 2011
[
close entry info
]
Hetero Components
(4, 79)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
3a: SULFATE ION (SO4a)
3aa: SULFATE ION (SO4aa)
3ab: SULFATE ION (SO4ab)
3ac: SULFATE ION (SO4ac)
3ad: SULFATE ION (SO4ad)
3ae: SULFATE ION (SO4ae)
3af: SULFATE ION (SO4af)
3ag: SULFATE ION (SO4ag)
3ah: SULFATE ION (SO4ah)
3ai: SULFATE ION (SO4ai)
3aj: SULFATE ION (SO4aj)
3ak: SULFATE ION (SO4ak)
3al: SULFATE ION (SO4al)
3am: SULFATE ION (SO4am)
3an: SULFATE ION (SO4an)
3ao: SULFATE ION (SO4ao)
3ap: SULFATE ION (SO4ap)
3aq: SULFATE ION (SO4aq)
3ar: SULFATE ION (SO4ar)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
3v: SULFATE ION (SO4v)
3w: SULFATE ION (SO4w)
3x: SULFATE ION (SO4x)
3y: SULFATE ION (SO4y)
3z: SULFATE ION (SO4z)
4a: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
MSE
30
Mod. Amino Acid
SELENOMETHIONINE
3
SO4
44
Ligand/Ion
SULFATE ION
4
TAM
1
Ligand/Ion
TRIS(HYDROXYETHYL)AMINOMETHANE
[
close Hetero Component info
]
Sites
(49, 49)
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)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:41 , MSE A:69 , TRP A:103 , ASP A:168 , ARG A:295
BINDING SITE FOR RESIDUE SO4 A 336
02
AC2
SOFTWARE
HIS A:47 , LYS A:48 , SER A:138 , PRO A:139
BINDING SITE FOR RESIDUE SO4 A 337
03
AC3
SOFTWARE
ARG A:110 , ASN A:111 , SO4 A:339
BINDING SITE FOR RESIDUE SO4 A 338
04
AC4
SOFTWARE
ARG A:110 , ASN A:111 , SO4 A:338
BINDING SITE FOR RESIDUE SO4 A 339
05
AC5
SOFTWARE
TRP A:97 , HIS A:122 , LYS A:126 , LYS A:149 , ALA A:150
BINDING SITE FOR RESIDUE SO4 A 340
06
AC6
SOFTWARE
LYS A:192 , PRO A:203 , ARG A:205
BINDING SITE FOR RESIDUE SO4 A 341
07
AC7
SOFTWARE
PRO A:42 , ALA A:104 , SER A:105 , GLN A:106 , PRO A:169 , ILE A:217 , HIS A:267 , GLN A:268
BINDING SITE FOR RESIDUE SO4 A 342
08
AC8
SOFTWARE
ASP B:26 , GLN B:28 , ASN B:82
BINDING SITE FOR RESIDUE SO4 B 335
09
AC9
SOFTWARE
PRO B:42 , ALA B:104 , SER B:105 , GLN B:106 , PRO B:169 , ALA B:216 , ILE B:217 , TRP B:218 , HIS B:267 , GLN B:268
BINDING SITE FOR RESIDUE SO4 B 336
10
BC1
SOFTWARE
ARG B:110 , ASN B:111 , LYS B:195
BINDING SITE FOR RESIDUE SO4 B 337
11
BC2
SOFTWARE
SER C:105 , GLN C:106 , PRO C:169 , ILE C:217 , TRP C:218 , HIS C:267 , GLN C:268
BINDING SITE FOR RESIDUE SO4 C 335
12
BC3
SOFTWARE
TRP C:97 , HIS C:122 , LYS C:126 , LYS C:149 , ALA C:150
BINDING SITE FOR RESIDUE SO4 C 336
13
BC4
SOFTWARE
LYS C:192 , ARG C:205
BINDING SITE FOR RESIDUE SO4 C 337
14
BC5
SOFTWARE
LYS C:194 , LYS C:195
BINDING SITE FOR RESIDUE SO4 C 338
15
BC6
SOFTWARE
ARG C:110 , ASN C:111 , LYS C:195
BINDING SITE FOR RESIDUE SO4 C 339
16
BC7
SOFTWARE
ASP D:41 , MSE D:69 , ALA D:104 , ARG D:295 , SO4 D:342
BINDING SITE FOR RESIDUE SO4 D 335
17
BC8
SOFTWARE
SER D:105 , GLN D:106 , ASP D:168 , PRO D:169 , ILE D:217 , TRP D:218 , HIS D:267 , GLN D:268
BINDING SITE FOR RESIDUE SO4 D 336
18
BC9
SOFTWARE
ARG D:110 , ASN D:111 , LYS D:195
BINDING SITE FOR RESIDUE SO4 D 337
19
CC1
SOFTWARE
HIS D:122 , LYS D:126 , LYS D:149 , ALA D:150
BINDING SITE FOR RESIDUE SO4 D 338
20
CC2
SOFTWARE
LYS D:194 , LYS D:195
BINDING SITE FOR RESIDUE SO4 D 339
21
CC3
SOFTWARE
ASP C:41 , PHE C:67 , MSE C:69 , ALA C:104 , ARG C:295 , SO4 C:343
BINDING SITE FOR RESIDUE SO4 C 340
22
CC4
SOFTWARE
LYS C:237 , GLU C:258 , VAL C:259 , THR D:316 , THR D:317
BINDING SITE FOR RESIDUE SO4 C 341
23
CC5
SOFTWARE
ALA A:285 , THR A:316 , GLU B:258 , VAL B:259
BINDING SITE FOR RESIDUE SO4 A 343
24
CC6
SOFTWARE
ASP D:26 , GLN D:28 , ASN D:82
BINDING SITE FOR RESIDUE SO4 D 340
25
CC7
SOFTWARE
ARG A:121 , GLY A:128 , PHE A:129 , ASP A:163
BINDING SITE FOR RESIDUE SO4 A 344
26
CC8
SOFTWARE
LYS B:192
BINDING SITE FOR RESIDUE SO4 B 338
27
CC9
SOFTWARE
HIS C:47 , LYS C:48 , SER C:138 , PRO C:139
BINDING SITE FOR RESIDUE SO4 C 342
28
DC1
SOFTWARE
LYS D:192 , ARG D:205
BINDING SITE FOR RESIDUE SO4 D 341
29
DC2
SOFTWARE
HIS B:47 , LYS B:48 , PRO B:139
BINDING SITE FOR RESIDUE SO4 B 339
30
DC3
SOFTWARE
TYR A:222 , GLN A:223
BINDING SITE FOR RESIDUE SO4 A 345
31
DC4
SOFTWARE
ASN D:185 , GLU D:215 , SO4 D:335
BINDING SITE FOR RESIDUE SO4 D 342
32
DC5
SOFTWARE
LYS A:194 , LYS A:195 , ASP A:201
BINDING SITE FOR RESIDUE SO4 A 346
33
DC6
SOFTWARE
ASN C:185 , GLU C:215 , THR C:265 , SO4 C:340
BINDING SITE FOR RESIDUE SO4 C 343
34
DC7
SOFTWARE
GLU D:301 , PHE D:303 , LYS D:311 , ARG D:312 , ILE D:313 , VAL D:314
BINDING SITE FOR RESIDUE SO4 D 343
35
DC8
SOFTWARE
LYS C:311 , ARG C:312
BINDING SITE FOR RESIDUE SO4 C 344
36
DC9
SOFTWARE
PRO D:188 , ILE D:207 , GLU D:208 , GLY D:209 , LEU D:210
BINDING SITE FOR RESIDUE SO4 D 344
37
EC1
SOFTWARE
PRO D:211 , GLU D:212
BINDING SITE FOR RESIDUE SO4 D 345
38
EC2
SOFTWARE
MSE C:242 , LYS C:253 , ASP C:307 , THR C:309
BINDING SITE FOR RESIDUE SO4 C 345
39
EC3
SOFTWARE
SER D:25 , ASP D:26
BINDING SITE FOR RESIDUE SO4 D 346
40
EC4
SOFTWARE
PHE C:234 , PRO D:288 , ASP D:289
BINDING SITE FOR RESIDUE SO4 D 347
41
EC5
SOFTWARE
LYS A:311 , ARG A:312
BINDING SITE FOR RESIDUE SO4 A 347
42
EC6
SOFTWARE
GLN A:292 , ASP B:62 , ASN B:63 , THR B:64 , ASP B:289
BINDING SITE FOR RESIDUE SO4 B 340
43
EC7
SOFTWARE
ILE C:271 , GLU C:272
BINDING SITE FOR RESIDUE SO4 C 346
44
EC8
SOFTWARE
ARG D:205 , ALA D:206
BINDING SITE FOR RESIDUE SO4 D 348
45
EC9
SOFTWARE
ASN C:31 , PRO C:32 , GLY C:261 , TYR C:281 , THR C:283 , ALA C:285 , SER C:298 , THR C:316 , LYS D:237 , GLU D:258 , VAL D:259
BINDING SITE FOR RESIDUE TAM C 347
46
FC1
SOFTWARE
ASN B:154 , THR B:157 , ASP B:165 , ASP B:166
BINDING SITE FOR RESIDUE CA B 341
47
FC2
SOFTWARE
ASN C:154 , THR C:157 , ASP C:165 , ASP C:166
BINDING SITE FOR RESIDUE CA C 348
48
FC3
SOFTWARE
ASN D:154 , THR D:157 , ASP D:165 , ASP D:166
BINDING SITE FOR RESIDUE CA D 349
49
FC4
SOFTWARE
ASN A:154 , THR A:157 , ASP A:165 , ASP A:166
BINDING SITE FOR RESIDUE CA A 348
[
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
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Glyco_hydro_43_3qedD01 (D:29-310)
1b: PFAM_Glyco_hydro_43_3qedD02 (D:29-310)
1c: PFAM_Glyco_hydro_43_3qedD03 (D:29-310)
1d: PFAM_Glyco_hydro_43_3qedD04 (D:29-310)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
B_Fructosidase
(34)
Family
:
Glyco_hydro_43
(11)
Cellvibrio japonicus (strain Ueda107) (Pseudomonas fluorescens subsp. cellulosa)
(3)
1a
Glyco_hydro_43-3qedD01
D:29-310
1b
Glyco_hydro_43-3qedD02
D:29-310
1c
Glyco_hydro_43-3qedD03
D:29-310
1d
Glyco_hydro_43-3qedD04
D:29-310
[
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
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 (211 KB)
Header - Asym.Unit
Biol.Unit 1 (54 KB)
Header - Biol.Unit 1
Biol.Unit 2 (55 KB)
Header - Biol.Unit 2
Biol.Unit 3 (55 KB)
Header - Biol.Unit 3
Biol.Unit 4 (55 KB)
Header - Biol.Unit 4
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
3QED
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
