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.
4CJ8
Asym. Unit
Info
Asym.Unit (676 KB)
Biol.Unit 1 (51 KB)
Biol.Unit 10 (50 KB)
Biol.Unit 11 (51 KB)
Biol.Unit 12 (50 KB)
Biol.Unit 13 (52 KB)
Biol.Unit 14 (50 KB)
Biol.Unit 15 (52 KB)
Biol.Unit 16 (51 KB)
Biol.Unit 2 (50 KB)
Biol.Unit 3 (52 KB)
Biol.Unit 4 (51 KB)
Biol.Unit 5 (52 KB)
Biol.Unit 6 (50 KB)
Biol.Unit 7 (50 KB)
Biol.Unit 8 (50 KB)
Biol.Unit 9 (51 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MONOCLINIC CRYSTAL FORM OF BOGT6A E192Q IN COMPLEX WITH UDP-GALNAC, UDP AND GALNAC
Authors
:
T. Pham, B. Stinson, N. Thiyagarajan, M. Lizotte-Waniewski, K. Brew, K. R. Acharya
Date
:
19 Dec 13 (Deposition) - 05 Feb 14 (Release) - 02 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: B (1x)
Biol. Unit 2: D (1x)
Biol. Unit 3: E (1x)
Biol. Unit 4: F (1x)
Biol. Unit 5: H (1x)
Biol. Unit 6: J (1x)
Biol. Unit 7: K (1x)
Biol. Unit 8: L (1x)
Biol. Unit 9: N (1x)
Biol. Unit 10: O (1x)
Biol. Unit 11: A (1x)
Biol. Unit 12: C (1x)
Biol. Unit 13: G (1x)
Biol. Unit 14: I (1x)
Biol. Unit 15: M (1x)
Biol. Unit 16: P (1x)
Keywords
:
Transferase, Monoclinic Form, Metal-Independent, Hydrolysed Products
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. T. K. Pham, B. Stinson, N. Thiyagarajan, M. Lizotte-Waniewski, K. Brew, K. R. Acharya
Structures Of Complexes Of A Metal-Independent Glycosyltransferase Gt6 From Bacteroides Ovatus With Udp-Galnac And Its Hydrolysis Products
J. Biol. Chem. V. 289 8041 2014
[
close entry info
]
Hetero Components
(7, 33)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
2a: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Ga)
2b: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gb)
2c: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gc)
2d: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gd)
2e: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Ge)
2f: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gf)
2g: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gg)
2h: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Gh)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
4a: N-ACETYL-D-GALACTOSAMINE (NGAa)
4b: N-ACETYL-D-GALACTOSAMINE (NGAb)
5a: SULFATE ION (SO4a)
6a: URIDINE-DIPHOSPHATE-N-ACETYLGALACT... (UD2a)
6b: URIDINE-DIPHOSPHATE-N-ACETYLGALACT... (UD2b)
6c: URIDINE-DIPHOSPHATE-N-ACETYLGALACT... (UD2c)
6d: URIDINE-DIPHOSPHATE-N-ACETYLGALACT... (UD2d)
6e: URIDINE-DIPHOSPHATE-N-ACETYLGALACT... (UD2e)
6f: URIDINE-DIPHOSPHATE-N-ACETYLGALACT... (UD2f)
7a: URIDINE-5'-DIPHOSPHATE (UDPa)
7b: URIDINE-5'-DIPHOSPHATE (UDPb)
7c: URIDINE-5'-DIPHOSPHATE (UDPc)
7d: URIDINE-5'-DIPHOSPHATE (UDPd)
7e: URIDINE-5'-DIPHOSPHATE (UDPe)
7f: URIDINE-5'-DIPHOSPHATE (UDPf)
7g: URIDINE-5'-DIPHOSPHATE (UDPg)
7h: URIDINE-5'-DIPHOSPHATE (UDPh)
7i: URIDINE-5'-DIPHOSPHATE (UDPi)
7j: URIDINE-5'-DIPHOSPHATE (UDPj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
A2G
8
Ligand/Ion
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
3
GOL
5
Ligand/Ion
GLYCEROL
4
NGA
2
Ligand/Ion
N-ACETYL-D-GALACTOSAMINE
5
SO4
1
Ligand/Ion
SULFATE ION
6
UD2
6
Ligand/Ion
URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
7
UDP
10
Ligand/Ion
URIDINE-5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(33, 33)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
1PE A:1240
BINDING SITE FOR RESIDUE GOL A1236
02
AC2
SOFTWARE
ILE A:8 , CYS A:9 , THR A:10 , TYR A:13 , ASN A:63 , TRP A:66 , ASN A:95 , ALA A:96 , LYS A:231 , HIS I:184
BINDING SITE FOR RESIDUE UDP A1237
03
AC3
SOFTWARE
HIS A:122 , TRP A:189 , GLN A:192
BINDING SITE FOR RESIDUE A2G A1238
04
AC4
SOFTWARE
LYS A:54
BINDING SITE FOR RESIDUE GOL A1239
05
AC5
SOFTWARE
GLN A:61 , GOL A:1236
BINDING SITE FOR RESIDUE 1PE A1240
06
AC6
SOFTWARE
ILE B:8 , CYS B:9 , THR B:10 , TYR B:13 , ASN B:63 , TRP B:66 , THR B:70 , ASN B:95 , ALA B:96 , LYS B:231 , HIS J:184
BINDING SITE FOR RESIDUE UDP B1237
07
AC7
SOFTWARE
HIS B:122 , TRP B:189 , GLN B:192 , HOH B:2002
BINDING SITE FOR RESIDUE A2G B1238
08
AC8
SOFTWARE
ARG B:2 , LYS B:54 , HIS B:55
BINDING SITE FOR RESIDUE SO4 B1239
09
AC9
SOFTWARE
ILE C:8 , CYS C:9 , THR C:10 , TYR C:13 , ASN C:69 , THR C:70 , ASN C:95 , ALA C:96 , LYS C:231 , HIS L:184
BINDING SITE FOR RESIDUE UDP C1237
10
BC1
SOFTWARE
HIS C:122 , PHE C:125 , GLN C:192 , HOH C:2001
BINDING SITE FOR RESIDUE A2G C1238
11
BC2
SOFTWARE
ILE D:8 , CYS D:9 , THR D:10 , TYR D:13 , TRP D:66 , ASN D:69 , THR D:70 , ASN D:95 , ALA D:96 , LYS D:231 , HIS K:184
BINDING SITE FOR RESIDUE UDP D1237
12
BC3
SOFTWARE
HIS D:122 , THR D:134 , TRP D:189 , GLN D:192
BINDING SITE FOR RESIDUE A2G D1238
13
BC4
SOFTWARE
ARG D:58
BINDING SITE FOR RESIDUE GOL D1239
14
BC5
SOFTWARE
ILE E:8 , CYS E:9 , THR E:10 , TYR E:13 , TRP E:66 , ASN E:69 , ARG E:73 , ASN E:95 , ALA E:96 , ALA E:155 , GLY E:156 , GLY E:157 , TRP E:189 , ASP E:191 , GLN E:192 , LYS E:231 , ARG E:243
BINDING SITE FOR RESIDUE UD2 E1246
15
BC6
SOFTWARE
ILE F:8 , CYS F:9 , THR F:10 , TYR F:13 , TRP F:66 , ASN F:69 , THR F:70 , ARG F:73 , ASN F:95 , ALA F:96 , ASN F:97 , HIS F:122 , ALA F:155 , GLY F:156 , GLY F:157 , TRP F:189 , ASP F:191 , GLN F:192 , LYS F:231 , ARG F:243
BINDING SITE FOR RESIDUE UD2 F1246
16
BC7
SOFTWARE
ILE G:8 , CYS G:9 , THR G:10 , TYR G:13 , TRP G:66 , ASN G:69 , THR G:70 , ARG G:73 , ASN G:95 , ALA G:96 , ALA G:155 , GLY G:156 , GLY G:157 , TRP G:189 , ASP G:191 , GLN G:192 , LYS G:231 , ARG G:243
BINDING SITE FOR RESIDUE UD2 G1246
17
BC8
SOFTWARE
ARG G:179 , ASN G:183
BINDING SITE FOR RESIDUE GOL G1247
18
BC9
SOFTWARE
ARG G:58
BINDING SITE FOR RESIDUE GOL G1248
19
CC1
SOFTWARE
ILE H:8 , CYS H:9 , THR H:10 , TYR H:13 , ASN H:69 , THR H:70 , ARG H:73 , ASN H:95 , ALA H:96 , ASN H:97 , ALA H:155 , GLY H:156 , GLY H:157 , TRP H:189 , ASP H:191 , GLN H:192 , LYS H:231 , ARG H:243
BINDING SITE FOR RESIDUE UD2 H1246
20
CC2
SOFTWARE
HIS A:184 , ILE I:8 , CYS I:9 , THR I:10 , TYR I:13 , THR I:70 , ASN I:95 , ALA I:96 , LYS I:231
BINDING SITE FOR RESIDUE UDP I1237
21
CC3
SOFTWARE
HIS I:122 , TRP I:189 , GLN I:192
BINDING SITE FOR RESIDUE A2G I1238
22
CC4
SOFTWARE
HIS B:184 , ILE J:8 , THR J:10 , TYR J:13 , ASN J:69 , THR J:70 , ASN J:95 , ALA J:96 , LYS J:231
BINDING SITE FOR RESIDUE UDP J1237
23
CC5
SOFTWARE
HIS J:122 , TRP J:189 , GLN J:192
BINDING SITE FOR RESIDUE A2G J1238
24
CC6
SOFTWARE
HIS D:184 , ILE K:8 , CYS K:9 , THR K:10 , TYR K:13 , ASN K:69 , THR K:70 , ASN K:95 , ALA K:96 , LYS K:231
BINDING SITE FOR RESIDUE UDP K1237
25
CC7
SOFTWARE
HIS K:122 , PHE K:125 , TRP K:189 , GLN K:192
BINDING SITE FOR RESIDUE A2G K1238
26
CC8
SOFTWARE
HIS C:184 , ILE L:8 , THR L:10 , TYR L:13 , TRP L:66 , ASN L:69 , ARG L:73 , ASN L:95 , ALA L:96 , LYS L:231 , HOH L:2002
BINDING SITE FOR RESIDUE UDP L1237
27
CC9
SOFTWARE
HIS L:122 , TRP L:189 , GLN L:192
BINDING SITE FOR RESIDUE A2G L1238
28
DC1
SOFTWARE
ILE M:8 , CYS M:9 , THR M:10 , TYR M:13 , TRP M:66 , ASN M:69 , ASN M:95 , ALA M:96 , LYS M:231 , HIS M:239 , ARG M:243 , NGA M:1247
BINDING SITE FOR RESIDUE UDP M1246
29
DC2
SOFTWARE
ASN M:95 , GLY M:156 , GLY M:157 , TRP M:189 , ASP M:191 , GLN M:192 , UDP M:1246
BINDING SITE FOR RESIDUE NGA M1247
30
DC3
SOFTWARE
ILE N:8 , THR N:10 , TYR N:13 , TRP N:66 , ASN N:95 , ALA N:96 , LYS N:231 , HIS N:239 , ARG N:243 , NGA N:1245
BINDING SITE FOR RESIDUE UDP N1244
31
DC4
SOFTWARE
ARG N:73 , ASN N:95 , GLY N:156 , GLY N:157 , ASP N:191 , GLN N:192 , UDP N:1244
BINDING SITE FOR RESIDUE NGA N1245
32
DC5
SOFTWARE
ILE O:8 , THR O:10 , LYS O:12 , TYR O:13 , TRP O:66 , ASN O:69 , ASN O:95 , ALA O:96 , ASN O:97 , GLY O:156 , GLY O:157 , ASP O:191 , GLN O:192 , LYS O:231
BINDING SITE FOR RESIDUE UD2 O1241
33
DC6
SOFTWARE
ILE P:8 , CYS P:9 , THR P:10 , TYR P:13 , TRP P:66 , ASN P:69 , ARG P:73 , ASN P:95 , ALA P:96 , ASN P:97 , ALA P:155 , GLY P:156 , GLY P:157 , TRP P:189 , HIS P:190 , ASP P:191 , GLN P:192 , LYS P:231 , ARG P:243
BINDING SITE FOR RESIDUE UD2 P1244
[
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
(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
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
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 (676 KB)
Header - Asym.Unit
Biol.Unit 1 (51 KB)
Header - Biol.Unit 1
Biol.Unit 10 (50 KB)
Header - Biol.Unit 10
Biol.Unit 11 (51 KB)
Header - Biol.Unit 11
Biol.Unit 12 (50 KB)
Header - Biol.Unit 12
Biol.Unit 13 (52 KB)
Header - Biol.Unit 13
Biol.Unit 14 (50 KB)
Header - Biol.Unit 14
Biol.Unit 15 (52 KB)
Header - Biol.Unit 15
Biol.Unit 16 (51 KB)
Header - Biol.Unit 16
Biol.Unit 2 (50 KB)
Header - Biol.Unit 2
Biol.Unit 3 (52 KB)
Header - Biol.Unit 3
Biol.Unit 4 (51 KB)
Header - Biol.Unit 4
Biol.Unit 5 (52 KB)
Header - Biol.Unit 5
Biol.Unit 6 (50 KB)
Header - Biol.Unit 6
Biol.Unit 7 (50 KB)
Header - Biol.Unit 7
Biol.Unit 8 (50 KB)
Header - Biol.Unit 8
Biol.Unit 9 (51 KB)
Header - Biol.Unit 9
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
4CJ8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
