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.
1OQM
Biol. Unit 1
Info
Asym.Unit (151 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (74 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
A 1:1 COMPLEX BETWEEN ALPHA-LACTALBUMIN AND BETA1,4-GALACTOSYLTRANSFERASE IN THE PRESENCE OF UDP-N-ACETYL-GALACTOSAMINE
Authors
:
B. Ramakrishnan, P. K. Qasba
Date
:
10 Mar 03 (Deposition) - 18 Mar 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Alpha-Lactalbumin, Beta1, 4-Galactosyltransferase, Udp- Galnac, Transferase, Biosynthetic Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Ramakrishnan, P. K. Qasba
Structure-Based Design Of Beta 1, 4-Galactosyltransferase I (Beta 4Gal-T1) With Equally Efficient N-Acetylgalactosaminyltransferase Activity: Point Mutation Broadens Beta 4Gal-T1 Donor Specificity.
J. Biol. Chem. V. 277 20833 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
3a: TETRAETHYLENE GLYCOL (PG4a)
3b: TETRAETHYLENE GLYCOL (PG4b)
4a: URIDINE-DIPHOSPHATE-N-ACETYLGALACT... (UD2a)
4b: URIDINE-DIPHOSPHATE-N-ACETYLGALACT... (UD2b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
MN
-1
Ligand/Ion
MANGANESE (II) ION
3
PG4
2
Ligand/Ion
TETRAETHYLENE GLYCOL
4
UD2
1
Ligand/Ion
URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:79 , ASP A:82 , GLU A:84 , ASP A:87 , ASP A:88 , HOH A:903 , HOH A:925
BINDING SITE FOR RESIDUE CA A 124
2
AC3
SOFTWARE
ASP B:254 , MET B:344 , HIS B:347 , UD2 B:404 , HOH B:989
BINDING SITE FOR RESIDUE MN B 403
3
AC5
SOFTWARE
PRO B:187 , PHE B:188 , ARG B:189 , ARG B:191 , PHE B:226 , ARG B:228 , ASP B:252 , VAL B:253 , ASP B:254 , LEU B:255 , MET B:277 , TYR B:289 , GLY B:292 , TRP B:314 , GLY B:315 , GLU B:317 , ASP B:318 , HIS B:347 , ASP B:350 , MN B:403 , HOH B:919 , HOH B:966 , HOH B:1284 , HOH B:1297 , HOH B:1465
BINDING SITE FOR RESIDUE UD2 B 404
4
AC7
SOFTWARE
PRO B:179 , HOH B:1264 , HOH B:1539
BINDING SITE FOR RESIDUE PG4 B 813
5
AC8
SOFTWARE
LYS A:114 , LEU A:115 , GLU A:116 , GLN A:117 , HOH A:1202 , HOH A:1506
BINDING SITE FOR RESIDUE PG4 A 814
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: LACTALBUMIN_LYSOZYME_2 (A:1-123)
2: LACTALBUMIN_LYSOZYME_1 (A:73-91)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LACTALBUMIN_LYSOZYME_2
PS51348
Alpha-lactalbumin / lysozyme C family profile.
LALBA_MOUSE
21-143
1
A:1-123
-
2
LACTALBUMIN_LYSOZYME_1
PS00128
Alpha-lactalbumin / lysozyme C signature.
LALBA_MOUSE
93-111
1
A:73-91
-
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d1oqma_ (A:)
1b: SCOP_d1oqmc_ (C:)
2a: SCOP_d1oqmb_ (B:)
2b: SCOP_d1oqmd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lysozyme-like
(1361)
Superfamily
:
Lysozyme-like
(1361)
Family
:
C-type lysozyme
(738)
Protein domain
:
alpha-Lactalbumin
(25)
Mouse (Mus musculus) [TaxId: 10090]
(12)
1a
d1oqma_
A:
1b
d1oqmc_
C:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
beta 1,4 galactosyltransferase (b4GalT1)
(39)
Protein domain
:
beta 1,4 galactosyltransferase (b4GalT1)
(20)
Cow (Bos taurus) [TaxId: 9913]
(20)
2a
d1oqmb_
B:
2b
d1oqmd_
D:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1oqmB00 (B:131-402)
1b: CATH_1oqmD00 (D:131-402)
2a: CATH_1oqmA00 (A:1-123)
2b: CATH_1oqmC00 (C:1-123)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Homologous Superfamily
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
House mouse (Mus musculus)
(18)
1a
1oqmB00
B:131-402
1b
1oqmD00
D:131-402
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Lysozyme
(1131)
Homologous Superfamily
:
[code=1.10.530.10, no name defined]
(605)
House mouse (Mus musculus)
(61)
2a
1oqmA00
A:1-123
2b
1oqmC00
C:1-123
[
close CATH info
]
Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Glyco_transf_7C_1oqmD01 (D:271-350)
1b: PFAM_Glyco_transf_7C_1oqmD02 (D:271-350)
2a: PFAM_Glyco_transf_7N_1oqmD03 (D:134-269)
2b: PFAM_Glyco_transf_7N_1oqmD04 (D:134-269)
3a: PFAM_Lys_1oqmC01 (C:1-120)
3b: PFAM_Lys_1oqmC02 (C:1-120)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GT-A
(172)
Family
:
Glyco_transf_7C
(16)
Bos taurus (Bovine)
(15)
1a
Glyco_transf_7C-1oqmD01
D:271-350
1b
Glyco_transf_7C-1oqmD02
D:271-350
Family
:
Glyco_transf_7N
(16)
Bos taurus (Bovine)
(15)
2a
Glyco_transf_7N-1oqmD03
D:134-269
2b
Glyco_transf_7N-1oqmD04
D:134-269
Clan
:
Lysozyme
(266)
Family
:
Lys
(245)
Mus musculus (Mouse)
(10)
3a
Lys-1oqmC01
C:1-120
3b
Lys-1oqmC02
C:1-120
[
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 (151 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (74 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
1OQM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help