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.
4KTR
Biol. Unit 2
Info
Asym.Unit (1.0 MB)
Biol.Unit 1 (269 KB)
Biol.Unit 2 (273 KB)
Biol.Unit 3 (269 KB)
Biol.Unit 4 (267 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 2-O-ALPHA-GLUCOSYLGLYCEROL PHOSPHORYLASE IN COMPLEX WITH ISOFAGOMINE AND GLYCEROL
Authors
:
K. K. Touhara, T. Nihira, M. Kitaoka, H. Nakai, S. Fushinobu
Date
:
21 May 13 (Deposition) - 21 May 14 (Release) - 12 Aug 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
(Alpha/Alpha)6 Barrel, Phosphorylase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. K. Touhara, T. Nihira, M. Kitaoka, H. Nakai, S. Fushinobu
Structural Basis For Reversible Phosphorolysis And Hydrolysis Reactions Of 2-O-Alpha-Glucosylglycerol Phosphorylase
J. Biol. Chem. V. 289 18067 2014
[
close entry info
]
Hetero Components
(7, 21)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
2a: 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHO... (7PEa)
2b: 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHO... (7PEb)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
3f: CALCIUM ION (CAf)
3g: CALCIUM ION (CAg)
4a: GLYCEROL (GOLa)
4aa: GLYCEROL (GOLaa)
4ab: GLYCEROL (GOLab)
4ac: GLYCEROL (GOLac)
4ad: GLYCEROL (GOLad)
4ae: GLYCEROL (GOLae)
4af: GLYCEROL (GOLaf)
4ag: GLYCEROL (GOLag)
4ah: GLYCEROL (GOLah)
4ai: GLYCEROL (GOLai)
4aj: GLYCEROL (GOLaj)
4ak: GLYCEROL (GOLak)
4al: GLYCEROL (GOLal)
4am: GLYCEROL (GOLam)
4an: GLYCEROL (GOLan)
4ao: GLYCEROL (GOLao)
4ap: GLYCEROL (GOLap)
4aq: GLYCEROL (GOLaq)
4ar: GLYCEROL (GOLar)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
4h: GLYCEROL (GOLh)
4i: GLYCEROL (GOLi)
4j: GLYCEROL (GOLj)
4k: GLYCEROL (GOLk)
4l: GLYCEROL (GOLl)
4m: GLYCEROL (GOLm)
4n: GLYCEROL (GOLn)
4o: GLYCEROL (GOLo)
4p: GLYCEROL (GOLp)
4q: GLYCEROL (GOLq)
4r: GLYCEROL (GOLr)
4s: GLYCEROL (GOLs)
4t: GLYCEROL (GOLt)
4u: GLYCEROL (GOLu)
4v: GLYCEROL (GOLv)
4w: GLYCEROL (GOLw)
4x: GLYCEROL (GOLx)
4y: GLYCEROL (GOLy)
4z: GLYCEROL (GOLz)
5a: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPER... (IFMa)
5b: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPER... (IFMb)
5c: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPER... (IFMc)
5d: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPER... (IFMd)
5e: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPER... (IFMe)
5f: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPER... (IFMf)
6a: HEXAETHYLENE GLYCOL (P6Ga)
6b: HEXAETHYLENE GLYCOL (P6Gb)
7a: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)... (PE4a)
8a: 3,6,9,12,15,18,21,24-OCTAOXAHEXACO... (PE5a)
9a: TETRAETHYLENE GLYCOL (PG4a)
9b: TETRAETHYLENE GLYCOL (PG4b)
9c: TETRAETHYLENE GLYCOL (PG4c)
9d: TETRAETHYLENE GLYCOL (PG4d)
10a: TRIETHYLENE GLYCOL (PGEa)
10b: TRIETHYLENE GLYCOL (PGEb)
10c: TRIETHYLENE GLYCOL (PGEc)
10d: TRIETHYLENE GLYCOL (PGEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
7PE
1
Ligand/Ion
2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
3
CA
-1
Ligand/Ion
CALCIUM ION
4
GOL
15
Ligand/Ion
GLYCEROL
5
IFM
1
Ligand/Ion
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
6
P6G
-1
Ligand/Ion
HEXAETHYLENE GLYCOL
7
PE4
1
Ligand/Ion
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
8
PE5
-1
Ligand/Ion
3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
9
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
10
PGE
1
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(29, 29)
Info
All Sites
01: AC7 (SOFTWARE)
02: CC4 (SOFTWARE)
03: CC5 (SOFTWARE)
04: CC6 (SOFTWARE)
05: CC7 (SOFTWARE)
06: CC8 (SOFTWARE)
07: CC9 (SOFTWARE)
08: DC1 (SOFTWARE)
09: DC2 (SOFTWARE)
10: DC3 (SOFTWARE)
11: DC4 (SOFTWARE)
12: DC5 (SOFTWARE)
13: DC6 (SOFTWARE)
14: DC7 (SOFTWARE)
15: DC8 (SOFTWARE)
16: DC9 (SOFTWARE)
17: EC1 (SOFTWARE)
18: EC2 (SOFTWARE)
19: EC3 (SOFTWARE)
20: EC4 (SOFTWARE)
21: EC5 (SOFTWARE)
22: EC6 (SOFTWARE)
23: EC7 (SOFTWARE)
24: EC8 (SOFTWARE)
25: EC9 (SOFTWARE)
26: FC1 (SOFTWARE)
27: GC9 (SOFTWARE)
28: HC3 (SOFTWARE)
29: HC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC7
SOFTWARE
ASP A:152 , GLU C:640 , ASP C:704
BINDING SITE FOR RESIDUE GOL A 807
02
CC4
SOFTWARE
GLU B:615 , HOH B:1107 , HOH B:1202 , ASP D:154 , HOH D:1055 , HOH D:1166
BINDING SITE FOR RESIDUE CA B 809
03
CC5
SOFTWARE
LYS C:65 , LYS C:69 , ARG C:371 , GLU C:389 , CYS C:391
BINDING SITE FOR RESIDUE 1PE C 801
04
CC6
SOFTWARE
ARG C:366 , GLU C:375 , GLY C:376 , GLU C:447 , ARG C:450 , HOH C:989
BINDING SITE FOR RESIDUE GOL C 802
05
CC7
SOFTWARE
ASP A:158 , TYR A:215 , THR C:555 , ILE C:557 , LYS C:561
BINDING SITE FOR RESIDUE GOL C 803
06
CC8
SOFTWARE
PHE C:332 , TRP C:333 , ASP C:334 , HOH C:1028 , HOH C:1100 , HOH C:1152
BINDING SITE FOR RESIDUE GOL C 804
07
CC9
SOFTWARE
GLU C:336 , LEU C:344 , TYR C:345 , TYR C:422 , VAL C:596 , PRO C:599 , GLN C:635 , GLN C:680 , ASN C:684 , VAL C:691 , HOH C:1150
BINDING SITE FOR RESIDUE PE4 C 805
08
DC1
SOFTWARE
GLY C:175 , LYS C:190
BINDING SITE FOR RESIDUE GOL C 806
09
DC2
SOFTWARE
GLU B:721 , ASP B:723 , ARG B:756 , GLU C:721 , ARG C:756
BINDING SITE FOR RESIDUE PGE C 807
10
DC3
SOFTWARE
TRP C:70 , ASN C:169 , ALA C:326 , TYR C:327 , GLN C:328 , PHE C:395 , THR C:665 , PHE C:666 , HOH C:997 , HOH C:1008
BINDING SITE FOR RESIDUE GOL C 808
11
DC4
SOFTWARE
PRO C:310 , LYS C:313 , LEU C:315 , ILE C:350 , ASN C:353 , ILE C:354 , HOH C:1169
BINDING SITE FOR RESIDUE GOL C 809
12
DC5
SOFTWARE
ASP A:154 , HOH A:979 , HOH A:1076 , GLU C:615 , HOH C:973 , HOH C:1148
BINDING SITE FOR RESIDUE CA C 810
13
DC6
SOFTWARE
ALA D:319 , PHE D:332 , TRP D:333 , ASP D:334 , GLN D:475 , GLN D:588 , LEU D:624 , GOL D:802 , HOH D:1015 , HOH D:1243
BINDING SITE FOR RESIDUE IFM D 801
14
DC7
SOFTWARE
TYR D:327 , TRP D:381 , PHE D:396 , GLN D:475 , IFM D:801 , HOH D:986 , HOH D:1185
BINDING SITE FOR RESIDUE GOL D 802
15
DC8
SOFTWARE
LYS D:65 , GLY D:68 , LYS D:69 , ARG D:371 , GLU D:389 , CYS D:391 , PRO D:392
BINDING SITE FOR RESIDUE PG4 D 803
16
DC9
SOFTWARE
ARG D:366 , GLU D:375 , GLY D:376 , GLU D:447 , ARG D:450 , HOH D:1069
BINDING SITE FOR RESIDUE GOL D 804
17
EC1
SOFTWARE
ASP B:704 , ASP D:152 , ALA D:231
BINDING SITE FOR RESIDUE GOL D 805
18
EC2
SOFTWARE
PRO D:182 , GLU D:212 , HOH D:1192 , HOH D:1202
BINDING SITE FOR RESIDUE GOL D 806
19
EC3
SOFTWARE
ASP D:539 , HIS D:541 , ILE D:543 , TYR D:551 , HOH D:1216 , GOL H:806
BINDING SITE FOR RESIDUE GOL D 807
20
EC4
SOFTWARE
GLU D:336 , MET D:340 , PRO D:341 , LEU D:344 , TYR D:422 , VAL D:596 , PRO D:599 , GLN D:635 , GLN D:680 , ASN D:684 , LEU D:689
BINDING SITE FOR RESIDUE 7PE D 808
21
EC5
SOFTWARE
LYS C:459 , TYR D:374 , HIS D:455 , VAL D:457 , MET D:468 , HOH D:1009 , HOH D:1052
BINDING SITE FOR RESIDUE GOL D 809
22
EC6
SOFTWARE
TRP D:70 , ASN D:169 , ALA D:326 , TYR D:327 , GLN D:328 , PHE D:395 , PHE D:666 , HOH D:958 , HOH D:976
BINDING SITE FOR RESIDUE GOL D 810
23
EC7
SOFTWARE
ARG D:366 , ARG D:367
BINDING SITE FOR RESIDUE GOL D 811
24
EC8
SOFTWARE
PRO D:310 , LYS D:313 , LEU D:315 , ILE D:350 , ILE D:354 , HOH D:1114
BINDING SITE FOR RESIDUE GOL D 812
25
EC9
SOFTWARE
GLU D:213 , ASP D:214 , HOH D:1176 , HOH D:1232 , HOH D:1247 , HOH D:1248
BINDING SITE FOR RESIDUE CA D 813
26
FC1
SOFTWARE
GLU D:615 , HOH D:1047 , HOH D:1067 , HOH D:1118 , ASP H:154
BINDING SITE FOR RESIDUE CA D 814
27
GC9
SOFTWARE
ASP C:209 , ALA C:210 , LYS G:605 , GLU G:608 , GLU G:612
BINDING SITE FOR RESIDUE GOL G 803
28
HC3
SOFTWARE
ASP C:154 , HOH C:1186 , GLU G:615 , HOH G:995 , HOH G:1097
BINDING SITE FOR RESIDUE CA G 806
29
HC9
SOFTWARE
GOL D:807 , GLU H:213 , ASP H:214 , HOH H:1098
BINDING SITE FOR RESIDUE GOL H 806
[
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
(, 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.
(no "Exon" information available for biological units yet)
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 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 (1.0 MB)
Header - Asym.Unit
Biol.Unit 1 (269 KB)
Header - Biol.Unit 1
Biol.Unit 2 (273 KB)
Header - Biol.Unit 2
Biol.Unit 3 (269 KB)
Header - Biol.Unit 3
Biol.Unit 4 (267 KB)
Header - Biol.Unit 4
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
4KTR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
