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.
3FEF
Biol. Unit 1
Info
Asym.Unit (293 KB)
Biol.Unit 1 (284 KB)
Biol.Unit 2 (145 KB)
Biol.Unit 3 (145 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 PUTATIVE GLUCOSIDASE LPLD FROM BACILLUS SUBTILIS
Authors
:
U. A. Ramagopal, K. R. Rajashankar, R. Toro, S. K. Burley, S. C. Almo, New Research Center For Structural Genomics (Nysgxrc)
Date
:
28 Nov 08 (Deposition) - 30 Dec 08 (Release) - 20 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,C (1x)
Biol. Unit 3: B,D (1x)
Keywords
:
Lpld, Gulosidase, Structural Genomics, Unknown Function, Glycosidase, Hydrolase, Manganese, Metal-Binding, Nad, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. A. Ramagopal, K. R. Rajashankar, R. Toro, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Glucosidase Lpld From Bacillu Subtilis.
To Be Published
[
close entry info
]
Hetero Components
(2, 39)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
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)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
MSE
32
Mod. Amino Acid
SELENOMETHIONINE
3
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:252 , ARG A:275 , ARG A:302 , HOH A:531 , HOH A:534
BINDING SITE FOR RESIDUE SO4 A 2
02
AC2
SOFTWARE
PRO A:284 , ARG C:429 , SER C:430
BINDING SITE FOR RESIDUE SO4 A 455
03
AC3
SOFTWARE
CYS A:173 , HIS A:210 , HOH A:457 , HOH A:469 , HOH A:758
BINDING SITE FOR RESIDUE MG A 1
04
AC4
SOFTWARE
PHE B:252 , ARG B:275 , ARG B:302 , HOH B:551 , HOH B:556
BINDING SITE FOR RESIDUE SO4 B 1
05
AC5
SOFTWARE
ARG B:429 , SER B:430 , PRO D:284
BINDING SITE FOR RESIDUE SO4 B 455
06
AC6
SOFTWARE
CYS B:173 , HIS B:210 , HOH B:765 , HOH B:766 , HOH B:767
BINDING SITE FOR RESIDUE MG B 456
07
AC7
SOFTWARE
PHE C:252 , ARG C:275 , ARG C:302
BINDING SITE FOR RESIDUE SO4 C 3
08
AC8
SOFTWARE
CYS C:173 , HIS C:210 , HOH C:455
BINDING SITE FOR RESIDUE MG C 1
09
AC9
SOFTWARE
PHE D:252 , ARG D:275 , ARG D:302
BINDING SITE FOR RESIDUE SO4 D 4
10
BC1
SOFTWARE
PRO B:284 , ARG D:429 , SER D:430
BINDING SITE FOR RESIDUE SO4 D 455
11
BC2
SOFTWARE
CYS D:173 , HIS D:210 , HOH D:760 , HOH D:761
BINDING SITE FOR RESIDUE MG D 1
[
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GLYCOSYL_HYDROL_F4 (A:142-173,B:142-173,C:142-173,D:14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLYCOSYL_HYDROL_F4
PS01324
Glycosyl hydrolases family 4 signature.
LPLD_BACSU
142-173
4
A:142-173
B:142-173
C:142-173
D:142-173
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3fefa2 (A:172-440)
1b: SCOP_d3fefb2 (B:172-440)
1c: SCOP_d3fefc2 (C:172-440)
1d: SCOP_d3fefd2 (D:172-440)
2a: SCOP_d3fefa1 (A:7-171)
2b: SCOP_d3fefc1 (C:7-171)
2c: SCOP_d3fefd1 (D:7-171)
2d: SCOP_d3fefb1 (B:7-171)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
AglA-like glucosidase
(9)
Protein domain
:
automated matches
(2)
Bacillus subtilis [TaxId: 1423]
(1)
1a
d3fefa2
A:172-440
1b
d3fefb2
B:172-440
1c
d3fefc2
C:172-440
1d
d3fefd2
D:172-440
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Bacillus subtilis [TaxId: 1423]
(11)
2a
d3fefa1
A:7-171
2b
d3fefc1
C:7-171
2c
d3fefd1
D:7-171
2d
d3fefb1
B:7-171
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (293 KB)
Header - Asym.Unit
Biol.Unit 1 (284 KB)
Header - Biol.Unit 1
Biol.Unit 2 (145 KB)
Header - Biol.Unit 2
Biol.Unit 3 (145 KB)
Header - Biol.Unit 3
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
3FEF
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help