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.
PLEASE WAIT...
Getting 'Exon' information from database.
1V84
Asym. Unit
Info
Asym.Unit (95 KB)
Biol.Unit 1 (90 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 GLCAT-P IN COMPLEX WITH N-ACETYLLACTOSAMINE, UDP, AND MN2+
Authors
:
S. Kakuda, T. Shiba, M. Ishiguro, H. Tagawa, S. Oka, Y. Kajihara, T. Kawa S. Wakatsuki, R. Kato
Date
:
27 Dec 03 (Deposition) - 25 May 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.82
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Transferase, Glycoprotein, Glycocyltransferase, Hnk-1 Epitope
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Kakuda, T. Shiba, M. Ishiguro, H. Tagawa, S. Oka, Y. Kajihara, T. Kawasaki, S. Wakatsuki, R. Kato
Structural Basis For Acceptor Substrate Recognition Of A Human Glucuronyltransferase, Glcat-P, An Enzyme Critical In The Biosynthesis Of The Carbohydrate Epitope Hnk-1
J. Biol. Chem. V. 279 22693 2004
[
close entry info
]
Hetero Components
(6, 9)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
1b: BETA-D-GALACTOSE (GALb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
5a: L(+)-TARTARIC ACID (TLAa)
6a: URIDINE-5'-DIPHOSPHATE (UDPa)
6b: URIDINE-5'-DIPHOSPHATE (UDPb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
2
Ligand/Ion
BETA-D-GALACTOSE
2
MN
2
Ligand/Ion
MANGANESE (II) ION
3
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5
TLA
1
Ligand/Ion
L(+)-TARTARIC ACID
6
UDP
2
Ligand/Ion
URIDINE-5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:228 , ARG A:249 , ILE A:253 , ASP A:254 , GLY A:281 , GLU A:284 , NDG A:506 , HOH A:522 , HOH A:529 , HOH A:532 , HOH A:618
BINDING SITE FOR RESIDUE GAL A 505
2
AC2
SOFTWARE
GLY A:223 , PHE A:245 , GLY A:280 , GLY A:281 , GAL A:505 , HOH A:604 , HOH A:605 , HOH A:619 , VAL B:320 , ASN B:321
BINDING SITE FOR RESIDUE NDG A 506
3
AC3
SOFTWARE
GLU B:228 , ARG B:249 , ILE B:253 , ASP B:254 , GLY B:281 , GLU B:284 , NAG B:508 , HOH B:618 , HOH B:636 , HOH B:708 , HOH B:709
BINDING SITE FOR RESIDUE GAL B 507
4
AC4
SOFTWARE
VAL A:320 , ASN A:321 , GLY B:223 , PHE B:245 , GLY B:280 , GAL B:507
BINDING SITE FOR RESIDUE NAG B 508
5
AC5
SOFTWARE
ASP A:197 , UDP A:503 , HOH A:507 , HOH A:508
BINDING SITE FOR RESIDUE MN A 501
6
AC6
SOFTWARE
ASP B:197 , UDP B:504 , HOH B:509 , HOH B:510
BINDING SITE FOR RESIDUE MN B 502
7
AC7
SOFTWARE
ARG A:231 , ARG A:240 , TRP A:241 , HIS A:248 , HOH A:648 , ARG B:213 , ARG B:263 , GLN B:267 , HOH B:610
BINDING SITE FOR RESIDUE TLA A 500
8
AC8
SOFTWARE
PRO A:91 , THR A:92 , TYR A:93 , ASP A:122 , LYS A:153 , ARG A:165 , GLY A:166 , ARG A:170 , ASP A:195 , ASP A:196 , ASP A:197 , HIS A:311 , ARG A:313 , MN A:501 , HOH A:528 , HOH A:581 , HOH A:620
BINDING SITE FOR RESIDUE UDP A 503
9
AC9
SOFTWARE
PRO B:91 , THR B:92 , TYR B:93 , ASP B:122 , ARG B:165 , GLY B:166 , ASP B:195 , ASP B:196 , ASP B:197 , HIS B:311 , ARG B:313 , MN B:502 , HOH B:550 , HOH B:683 , HOH B:709
BINDING SITE FOR RESIDUE UDP B 504
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_044538 (A131T, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_044538
A
131
T
B3GA1_HUMAN
Polymorphism
35434644
A/B
A
131
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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
(3, 6)
Info
All Exons
Exon 1.4c (A:83-207 (gaps) | B:82-207 (gaps))
Exon 1.5 (A:208-306 | B:208-306)
Exon 1.6 (A:307-334 | B:307-334)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3d/1.4c
2: Boundary 1.4c/1.5
3: Boundary 1.5/1.6
4: Boundary 1.6/1.8b
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000392580
1
ENSE00000999945
chr11:
134281812-134281701
112
B3GA1_HUMAN
-
0
0
-
-
1.3b
ENST00000392580
3b
ENSE00001512424
chr11:
134257834-134257721
114
B3GA1_HUMAN
-
0
0
-
-
1.3d
ENST00000392580
3d
ENSE00001512423
chr11:
134257588-134257442
147
B3GA1_HUMAN
1-38
38
0
-
-
1.4c
ENST00000392580
4c
ENSE00000749062
chr11:
134254082-134253574
509
B3GA1_HUMAN
38-207
170
2
A:83-207 (gaps)
B:82-207 (gaps)
125
126
1.5
ENST00000392580
5
ENSE00000749063
chr11:
134252900-134252604
297
B3GA1_HUMAN
208-306
99
2
A:208-306
B:208-306
99
99
1.6
ENST00000392580
6
ENSE00000800138
chr11:
134251918-134251818
101
B3GA1_HUMAN
307-334
28
2
A:307-334
B:307-334
28
28
1.8b
ENST00000392580
8b
ENSE00001387274
chr11:
134250641-134248400
2242
B3GA1_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1v84a_ (A:)
1b: SCOP_d1v84b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
1,3-glucuronyltransferase
(7)
Protein domain
:
Beta-1,3-glucuronyltransferase 1, GlcAT-P
(3)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1v84a_
A:
1b
d1v84b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1v84A00 (A:83-334)
1b: CATH_1v84B00 (B:82-334)
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)
Human (Homo sapiens)
(73)
1a
1v84A00
A:83-334
1b
1v84B00
B:82-334
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Glyco_transf_43_1v84B01 (B:105-316)
1b: PFAM_Glyco_transf_43_1v84B02 (B:105-316)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GT-A
(172)
Family
:
Glyco_transf_43
(4)
Homo sapiens (Human)
(4)
1a
Glyco_transf_43-1v84B01
B:105-316
1b
Glyco_transf_43-1v84B02
B:105-316
[
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 (95 KB)
Header - Asym.Unit
Biol.Unit 1 (90 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
1V84
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
