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.
3A22
Biol. Unit 2
Info
Asym.Unit (225 KB)
Biol.Unit 1 (113 KB)
Biol.Unit 2 (112 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF BETA-L-ARABINOPYRANOSIDASE COMPLEXED WITH L-ARABINOSE
Authors
:
Z. Fujimoto, H. Ichinose, S. Kaneko
Date
:
27 Apr 09 (Deposition) - 14 Jul 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Beta-Alpha-Barrel, Greek Key Motif, Beta-Jellyroll, Beta-Trefoil, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Ichinose, Z. Fujimoto, M. Honda, K. Harazono, Y. Nishimoto, A. Uzura, S. Kaneko
A Beta-L-Arabinopyranosidase From Streptomyces Avermitilis Is A Novel Member Of Glycoside Hydrolase Family 27.
J. Biol. Chem. V. 284 25097 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 16)
Info
All Hetero Components
1a: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGa)
1b: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGb)
1c: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGc)
1d: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHO... (1PGd)
2a: ALPHA-L-ARABINOSE (ARAa)
2b: ALPHA-L-ARABINOSE (ARAb)
2c: ALPHA-L-ARABINOSE (ARAc)
2d: ALPHA-L-ARABINOSE (ARAd)
2e: ALPHA-L-ARABINOSE (ARAe)
2f: ALPHA-L-ARABINOSE (ARAf)
2g: ALPHA-L-ARABINOSE (ARAg)
2h: ALPHA-L-ARABINOSE (ARAh)
2i: ALPHA-L-ARABINOSE (ARAi)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
4l: GLYCEROL (GOLl)
4m: GLYCEROL (GOLm)
4n: GLYCEROL (GOLn)
4o: GLYCEROL (GOLo)
4p: GLYCEROL (GOLp)
4q: GLYCEROL (GOLq)
4r: GLYCEROL (GOLr)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PG
2
Ligand/Ion
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2
ARA
4
Ligand/Ion
ALPHA-L-ARABINOSE
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
GOL
8
Ligand/Ion
GLYCEROL
5
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC7 (SOFTWARE)
03: BC1 (SOFTWARE)
04: BC2 (SOFTWARE)
05: BC4 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC8 (SOFTWARE)
09: BC9 (SOFTWARE)
10: CC2 (SOFTWARE)
11: CC3 (SOFTWARE)
12: CC4 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC6 (SOFTWARE)
15: CC7 (SOFTWARE)
16: CC8 (SOFTWARE)
17: CC9 (SOFTWARE)
18: DC1 (SOFTWARE)
19: DC2 (SOFTWARE)
20: DC3 (SOFTWARE)
21: DC4 (SOFTWARE)
22: DC5 (SOFTWARE)
23: DC6 (SOFTWARE)
24: DC7 (SOFTWARE)
25: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
ASP A:587 , ALA A:588 , TYR A:589 , ASN A:590 , TRP A:602 , ASN A:605 , GLN A:607 , ASN A:609 , HOH A:1177 , ASN B:553 , TRP B:602
BINDING SITE FOR RESIDUE ARA A 721
02
AC7
SOFTWARE
ARG A:49 , THR A:490 , GLY A:491 , ALA A:492 , SER A:493 , HIS B:131 , GLY B:134 , LEU B:135 , HOH B:1092 , HOH B:1240
BINDING SITE FOR RESIDUE GOL A 912
03
BC1
SOFTWARE
THR A:411 , GLY A:412 , TYR A:413 , THR A:414 , HOH A:939 , SO4 A:971 , ALA B:393 , SER B:394
BINDING SITE FOR RESIDUE GOL A 917
04
BC2
SOFTWARE
CYS A:148 , TYR A:152 , CYS A:188 , TRP A:226 , ASP A:247 , TYR A:250 , ARA A:701 , HOH A:1004 , HOH A:1300 , THR B:593 , HOH B:747
BINDING SITE FOR RESIDUE GOL A 919
05
BC4
SOFTWARE
THR A:258 , SER A:259 , SER A:262 , HOH A:1038 , HOH A:1261 , LEU B:591 , HOH B:1189
BINDING SITE FOR RESIDUE GOL A 926
06
BC6
SOFTWARE
SER A:493 , ALA A:494 , HOH A:759 , LYS B:136
BINDING SITE FOR RESIDUE GOL A 930
07
BC7
SOFTWARE
TYR A:72 , PRO A:120 , GLY A:436 , TYR A:438 , THR A:450 , HOH A:978 , HOH A:1051 , HOH A:1361 , ASN B:466
BINDING SITE FOR RESIDUE 1PG A 962
08
BC8
SOFTWARE
PRO A:153 , TYR A:251 , ASN A:253 , HOH A:1146 , VAL B:623 , ALA B:625 , GLY B:626
BINDING SITE FOR RESIDUE 1PG A 964
09
BC9
SOFTWARE
SER A:409 , ALA A:410 , THR A:411 , HOH A:772 , GOL A:917 , HOH A:1053 , ALA B:393 , THR B:431 , HOH B:915 , HOH B:1207
BINDING SITE FOR RESIDUE SO4 A 971
10
CC2
SOFTWARE
TRP B:63 , ASP B:98 , GLU B:99 , TYR B:140 , CYS B:148 , LYS B:184 , ASP B:186 , CYS B:224 , TRP B:226 , ARG B:243 , ASP B:247 , MET B:283 , HOH B:716 , GOL B:928
BINDING SITE FOR RESIDUE ARA B 751
11
CC3
SOFTWARE
THR B:481 , ASP B:545 , ILE B:546 , TYR B:547 , ASN B:548 , TRP B:560 , ASN B:563 , ASN B:567 , HOH B:736 , HOH B:750
BINDING SITE FOR RESIDUE ARA B 761
12
CC4
SOFTWARE
ASN A:553 , TRP A:602 , ASP B:587 , TYR B:589 , ASN B:590 , LEU B:591 , TRP B:602 , ASN B:605 , GLN B:607 , ASN B:609
BINDING SITE FOR RESIDUE ARA B 771
13
CC5
SOFTWARE
ASP B:630 , ALA B:631 , TYR B:632 , ASN B:633 , TRP B:645 , THR B:649 , ASN B:652 , 1PG B:966 , HOH B:1036 , HOH B:1065
BINDING SITE FOR RESIDUE ARA B 781
14
CC6
SOFTWARE
ALA B:348 , GLU B:349 , ASP B:350 , THR B:351 , LEU B:354 , ILE B:381 , THR B:382 , HOH B:860 , HOH B:1178
BINDING SITE FOR RESIDUE GOL B 913
15
CC7
SOFTWARE
THR A:292 , HOH A:803 , THR B:320 , SER B:321 , GLU B:322 , HOH B:1351
BINDING SITE FOR RESIDUE GOL B 916
16
CC8
SOFTWARE
GLU B:349 , THR B:352 , ARG B:575 , GLU B:577 , GLY B:582 , CYS B:604 , HOH B:1016 , HOH B:1256
BINDING SITE FOR RESIDUE GOL B 918
17
CC9
SOFTWARE
ASP B:71 , TYR B:72 , SER B:73 , GLU B:118 , PRO B:120 , LYS B:505 , 1PG B:963 , HOH B:1131 , HOH B:1135
BINDING SITE FOR RESIDUE GOL B 920
18
DC1
SOFTWARE
PRO B:54 , THR B:275 , GLY B:276 , HOH B:782 , HOH B:783 , HOH B:784 , HOH B:894
BINDING SITE FOR RESIDUE GOL B 922
19
DC2
SOFTWARE
THR A:593 , TYR B:152 , CYS B:188 , ASP B:247 , TYR B:250 , ARA B:751 , HOH B:823 , HOH B:1308
BINDING SITE FOR RESIDUE GOL B 928
20
DC3
SOFTWARE
GLY A:166 , HIS A:167 , TYR A:168 , ASP A:169 , HOH A:1016 , HOH A:1263 , HOH B:1096
BINDING SITE FOR RESIDUE GOL B 932
21
DC4
SOFTWARE
SER B:256 , MET B:257 , THR B:258 , HOH B:1180
BINDING SITE FOR RESIDUE GOL B 934
22
DC5
SOFTWARE
ALA A:294 , ARG A:297 , GLU A:322 , ALA B:85 , LEU B:316 , MET B:319 , SER B:321 , ALA B:324 , LYS B:328 , HOH B:738 , HOH B:757 , HOH B:1073 , HOH B:1114
BINDING SITE FOR RESIDUE EPE B 951
23
DC6
SOFTWARE
TYR B:72 , PRO B:120 , ALA B:434 , GLY B:435 , THR B:450 , GOL B:920 , HOH B:1055
BINDING SITE FOR RESIDUE 1PG B 963
24
DC7
SOFTWARE
ALA A:192 , ARG A:542 , HOH A:723 , HOH A:1032 , ASN B:595 , TYR B:632 , ASN B:633 , TRP B:645 , ARA B:781 , HOH B:1005 , HOH B:1007
BINDING SITE FOR RESIDUE 1PG B 966
25
DC8
SOFTWARE
ARG B:471 , GLY B:515 , GLY B:516 , HOH B:694 , HOH B:1386 , HOH B:1387
BINDING SITE FOR RESIDUE SO4 B 972
[
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
(2, 4)
Info
all CATH domains
1a: CATH_3a22B01 (B:47-339)
1b: CATH_3a22A01 (A:45-339)
2a: CATH_3a22A04 (A:532-658)
2b: CATH_3a22B04 (B:532-658)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Streptomyces avermitilis. Organism_taxid: 33903. Strain: nbrc14893.
(3)
1a
3a22B01
B:47-339
1b
3a22A01
A:45-339
Class
:
Mainly Beta
(13760)
Architecture
:
Trefoil
(289)
Topology
:
Trefoil (Acidic Fibroblast Growth Factor, subunit A)
(289)
Homologous Superfamily
:
[code=2.80.10.50, no name defined]
(289)
Streptomyces avermitilis. Organism_taxid: 33903. Strain: nbrc14893.
(3)
2a
3a22A04
A:532-658
2b
3a22B04
B:532-658
[
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 B
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 (225 KB)
Header - Asym.Unit
Biol.Unit 1 (113 KB)
Header - Biol.Unit 1
Biol.Unit 2 (112 KB)
Header - Biol.Unit 2
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
3A22
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
