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...
Getting 'PROSITE' information from database.
3MBG
Biol. Unit 1
Info
Asym.Unit (77 KB)
Biol.Unit 1 (47 KB)
Biol.Unit 2 (47 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 HUMAN AUGMENTER OF LIVER REGENERATION (ALR)
Authors
:
M. Dong, S. Schaefer, V. N. Daithankar, C. Thorpe, B. J. Bahnson
Date
:
25 Mar 10 (Deposition) - 21 Jul 10 (Release) - 25 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (2x)
Biol. Unit 2: B,C (1x)
Keywords
:
Flavin, Flavoprotein, Sulfhydryl Oxidase, Fad, Gfer, Alr
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. N. Daithankar, S. A. Schaefer, M. Dong, B. J. Bahnson, C. Thorpe
Structure Of The Human Sulfhydryl Oxidase Augmenter Of Live Regeneration And Characterization Of A Human Mutation Causing An Autosomal Recessive Myopathy .
Biochemistry V. 49 6737 2010
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
1j: ACETATE ION (ACTj)
1k: ACETATE ION (ACTk)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
4i: ZINC ION (ZNi)
4j: ZINC ION (ZNj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
10
Ligand/Ion
ACETATE ION
2
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
NA
-1
Ligand/Ion
SODIUM ION
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
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: BC4 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC2 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC6 (SOFTWARE)
13: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ZN A:3 , HOH A:22 , HOH A:27 , HOH A:47 , HOH A:59 , HOH A:64 , ARG A:99 , GLU A:100 , GLY A:103 , ARG A:104 , TRP A:107 , HIS A:111 , CYS A:145 , LEU A:149 , CYS A:171 , HIS A:174 , ASN A:175 , VAL A:177 , ASN A:178 , LYS A:180 , LEU A:181 , LYS A:183 , PHE A:186 , ARG A:194 , TRP A:195 , ACT A:207 , HOH A:211 , HOH A:232 , HOH A:439 , ASP B:159 , ARG B:161 , HOH B:229
BINDING SITE FOR RESIDUE FAD A 300
02
AC2
SOFTWARE
ASP A:159 , ACT A:206 , GLU C:100 , FAD C:300 , HOH C:441
BINDING SITE FOR RESIDUE ZN A 2
03
AC3
SOFTWARE
GLU A:100 , ACT A:207 , FAD A:300 , HOH A:439 , ASP B:159
BINDING SITE FOR RESIDUE ZN A 3
04
AC4
SOFTWARE
ASP A:98
BINDING SITE FOR RESIDUE NA A 9
05
AC5
SOFTWARE
GLU A:101 , HIS A:105 , ACT A:600 , ACT A:700
BINDING SITE FOR RESIDUE ZN A 1
06
AC6
SOFTWARE
ZN A:1 , HOH A:28 , GLU A:101 , ARG A:104 , HIS A:105 , ACT A:700
BINDING SITE FOR RESIDUE ACT A 600
07
AC7
SOFTWARE
ZN A:1 , GLU A:101 , HIS A:105 , ACT A:600
BINDING SITE FOR RESIDUE ACT A 700
08
BC4
SOFTWARE
ZN A:2 , HOH A:7 , ASP A:159 , ARG A:161 , ACT A:206 , HOH B:307 , ARG C:99 , GLU C:100 , GLY C:103 , ARG C:104 , TRP C:107 , HIS C:111 , CYS C:145 , LEU C:149 , CYS C:171 , HIS C:174 , ASN C:175 , VAL C:177 , ASN C:178 , LYS C:180 , LEU C:181 , LYS C:183 , PHE C:186 , ARG C:194 , TRP C:195 , HOH C:280 , HOH C:291 , HOH C:323 , HOH C:325 , HOH C:359 , HOH C:441
BINDING SITE FOR RESIDUE FAD C 300
09
CC1
SOFTWARE
ZN A:2 , ASP A:159 , ARG A:161 , THR A:162 , ALA A:165 , GLU C:100 , LYS C:183 , FAD C:300
BINDING SITE FOR RESIDUE ACT A 206
10
CC2
SOFTWARE
ZN A:3 , GLU A:100 , LYS A:183 , FAD A:300 , ASP B:159 , ARG B:161 , THR B:162 , ALA B:165
BINDING SITE FOR RESIDUE ACT A 207
11
CC5
SOFTWARE
GLU A:147 , HIS B:172 , GLU B:176 , ARG B:179
BINDING SITE FOR RESIDUE ZN B 2
12
CC6
SOFTWARE
HIS A:172 , GLU A:176 , ARG A:179 , GLU C:147
BINDING SITE FOR RESIDUE ZN A 208
13
DC1
SOFTWARE
HIS A:134 , HIS A:157 , PRO A:158 , HOH A:471
BINDING SITE FOR RESIDUE ACT A 500
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_061994 (F166L, chain A, )
2: VAR_063435 (R194H, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_061994
F
166
L
ALR_HUMAN
Polymorphism
36041021
A
F
166
L
2
UniProt
VAR_063435
R
194
H
ALR_HUMAN
Disease (MPMCHD)
121908192
A
R
194
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ERV_ALR (A:95-195)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ERV_ALR
PS51324
ERV/ALR sulfhydryl oxidase domain profile.
ALR_HUMAN
95-195
2
A:95-195
-
-
[
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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3mbga_ (A:)
1b: SCOP_d3mbgb_ (B:)
1c: SCOP_d3mbgc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
FAD-dependent thiol oxidase
(15)
Family
:
FAD-dependent thiol oxidase
(10)
Protein domain
:
Augmenter of liver regeneration
(7)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d3mbga_
A:
1b
d3mbgb_
B:
1c
d3mbgc_
C:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_Evr1_Alr_3mbgC01 (C:104-197)
1b: PFAM_Evr1_Alr_3mbgC02 (C:104-197)
1c: PFAM_Evr1_Alr_3mbgC03 (C:104-197)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Evr1_Alr]
(7)
Family
:
Evr1_Alr
(7)
Homo sapiens (Human)
(4)
1a
Evr1_Alr-3mbgC01
C:104-197
1b
Evr1_Alr-3mbgC02
C:104-197
1c
Evr1_Alr-3mbgC03
C:104-197
[
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
Asymmetric Unit 1
Asymmetric Unit 2
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 (77 KB)
Header - Asym.Unit
Biol.Unit 1 (47 KB)
Header - Biol.Unit 1
Biol.Unit 2 (47 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
3MBG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
