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.
3BGA
Asym. Unit
Info
Asym.Unit (357 KB)
Biol.Unit 1 (348 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-GALACTOSIDASE FROM BACTEROIDES THETAIOTAOMICRON VPI-5482
Authors
:
D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
26 Nov 07 (Deposition) - 11 Dec 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Beta-Galactosidase, Nysgxrc, Protein Structure Initiative Ii (Psi-Ii), Glycosyl Hydrolase Family 2, Jelly-Roll Fold, Immunoglobulin-Like Fold, Tim-Barrel Domain, Structural Genomics, New York Sgx Research Center For Structural Genomics
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Kumaran, S. K. Burley, S. Swaminathan
Crystal Structure Analysis Of Beta-Galactosidase From Bacteroides Thetaiotaomicron Vpi-5482.
To Be Published
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 48)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3ag: SELENOMETHIONINE (MSEag)
3ah: SELENOMETHIONINE (MSEah)
3ai: SELENOMETHIONINE (MSEai)
3aj: SELENOMETHIONINE (MSEaj)
3ak: SELENOMETHIONINE (MSEak)
3al: SELENOMETHIONINE (MSEal)
3am: SELENOMETHIONINE (MSEam)
3an: SELENOMETHIONINE (MSEan)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
MSE
40
Mod. Amino Acid
SELENOMETHIONINE
4
NA
4
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:438 , HIS A:440 , GLU A:484 , HOH A:1476 , HOH A:1477 , HOH A:1478
BINDING SITE FOR RESIDUE MG A 1
2
AC2
SOFTWARE
GLU B:438 , HIS B:440 , GLU B:484 , HOH B:1462 , HOH B:1463 , HOH B:1465
BINDING SITE FOR RESIDUE MG B 2
3
AC3
SOFTWARE
ASP B:227 , PHE B:614 , ASN B:617 , HOH B:1039 , HOH B:1603
BINDING SITE FOR RESIDUE NA B 3
4
AC4
SOFTWARE
ASP A:227 , PHE A:614 , ASN A:617 , HOH A:1054 , HOH A:1589
BINDING SITE FOR RESIDUE NA A 4
5
AC5
SOFTWARE
PRO B:924 , LEU B:966 , GLU B:967 , ALA B:969 , HOH B:1470 , HOH B:1547
BINDING SITE FOR RESIDUE NA B 5
6
AC6
SOFTWARE
PRO A:924 , LEU A:966 , GLU A:967 , ALA A:969 , HOH A:1099 , HOH A:1520
BINDING SITE FOR RESIDUE NA A 6
7
AC7
SOFTWARE
LYS A:192 , THR A:193 , ASN A:436 , HOH A:1179
BINDING SITE FOR RESIDUE CL A 7
8
AC8
SOFTWARE
LYS B:192 , THR B:193 , ASN B:436
BINDING SITE FOR RESIDUE CL B 8
[
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
(4, 10)
Info
all CATH domains
1a: CATH_3bgaA03 (A:357-637)
1b: CATH_3bgaB03 (B:357-637)
2a: CATH_3bgaA05 (A:754-1023)
2b: CATH_3bgaB05 (B:754-1022)
3a: CATH_3bgaA02 (A:246-356)
3b: CATH_3bgaB02 (B:246-356)
3c: CATH_3bgaA04 (A:638-742)
3d: CATH_3bgaB04 (B:638-742)
4a: CATH_3bgaA01 (A:27-245)
4b: CATH_3bgaB01 (B:23-245)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Glycosidases
(843)
Bacteroides thetaiotaomicron vpi-5482. Organism_taxid: 226186. Strain:vpi-5482, dsm 2079, nctc 10582, e50.
(1)
1a
3bgaA03
A:357-637
1b
3bgaB03
B:357-637
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 vpi-5482. Organism_taxid: 226186. Strain:vpi-5482, dsm 2079, nctc 10582, e50.
(1)
2a
3bgaA05
A:754-1023
2b
3bgaB05
B:754-1022
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.320, no name defined]
(46)
Bacteroides thetaiotaomicron vpi-5482. Organism_taxid: 226186. Strain:vpi-5482, dsm 2079, nctc 10582, e50.
(1)
3a
3bgaA02
A:246-356
3b
3bgaB02
B:246-356
3c
3bgaA04
A:638-742
3d
3bgaB04
B:638-742
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Galactose-binding domain-like
(195)
Bacteroides thetaiotaomicron vpi-5482. Organism_taxid: 226186. Strain:vpi-5482, dsm 2079, nctc 10582, e50.
(1)
4a
3bgaA01
A:27-245
4b
3bgaB01
B:23-245
[
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 A
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 (357 KB)
Header - Asym.Unit
Biol.Unit 1 (348 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
3BGA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
