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.
3AML
Asym. Unit
Info
Asym.Unit (264 KB)
Biol.Unit 1 (256 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE STARCH BRANCHING ENZYME I (BEI) FROM ORYZA SATIVA L
Authors
:
Y. Kakuta, K. Chaen, J. Noguchi, N. Vu, M. Kimura
Date
:
20 Aug 10 (Deposition) - 28 Sep 11 (Release) - 28 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Starch-Branching, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Noguchi, K. Chaen, N. T. Vu, T. Akasaka, H. Shimada, T. Nakashima, A. Nishi, H. Satoh, T. Omori, Y. Kakuta, M. Kimura
Crystal Structure Of The Branching Enzyme I (Bei) From Oryz Sativa L With Implications For Catalysis And Substrate Binding.
Glycobiology V. 21 1108 2011
[
close entry info
]
Hetero Components
(5, 38)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: BETA-MERCAPTOETHANOL (BMEa)
2b: BETA-MERCAPTOETHANOL (BMEb)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4a: GLYCEROL (GOLa)
4aa: GLYCEROL (GOLaa)
4ab: GLYCEROL (GOLab)
4ac: GLYCEROL (GOLac)
4ad: GLYCEROL (GOLad)
4ae: GLYCEROL (GOLae)
4af: GLYCEROL (GOLaf)
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: SUCCINIC ACID (SINa)
5b: SUCCINIC ACID (SINb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
BME
2
Ligand/Ion
BETA-MERCAPTOETHANOL
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
GOL
32
Ligand/Ion
GLYCEROL
5
SIN
2
Ligand/Ion
SUCCINIC ACID
[
close Hetero Component info
]
Sites
(38, 38)
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)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:421 , LEU A:422 , ALA A:423 , ASN A:453 , ARG A:454 , CYS A:460 , SIN A:766
BINDING SITE FOR RESIDUE BME A 756
02
AC2
SOFTWARE
GLU A:185 , ARG A:342 , GLU A:399 , SER A:466 , HIS A:467 , HOH A:1166
BINDING SITE FOR RESIDUE GOL A 757
03
AC3
SOFTWARE
HIS A:44 , PHE A:100 , TRP A:319 , GLU A:320 , GOL A:780 , HOH A:995 , HOH A:1004 , HOH A:1307
BINDING SITE FOR RESIDUE EPE A 758
04
AC4
SOFTWARE
ARG A:174 , LYS A:307 , MET A:333 , ASP A:334 , ASN A:357 , LEU A:390 , HOH A:799 , HOH A:1069
BINDING SITE FOR RESIDUE GOL A 759
05
AC5
SOFTWARE
ASP A:492 , ARG A:563 , GOL A:764 , HOH A:1390
BINDING SITE FOR RESIDUE GOL A 760
06
AC6
SOFTWARE
GLY A:473
BINDING SITE FOR RESIDUE ACT A 761
07
AC7
SOFTWARE
ASN A:384 , HIS A:388 , PRO A:410 , VAL A:411 , ASP A:412 , GLY A:417 , HOH A:1155 , HOH A:1243
BINDING SITE FOR RESIDUE GOL A 762
08
AC8
SOFTWARE
ASP A:36 , CYS A:39 , LEU A:40
BINDING SITE FOR RESIDUE BME A 763
09
AC9
SOFTWARE
ARG A:563 , TYR A:566 , LEU A:642 , GLY A:646 , GOL A:760 , GOL A:765
BINDING SITE FOR RESIDUE GOL A 764
10
BC1
SOFTWARE
TYR A:566 , LEU A:642 , GOL A:764 , GOL A:770 , HOH A:857
BINDING SITE FOR RESIDUE GOL A 765
11
BC2
SOFTWARE
ASP A:400 , GLY A:403 , ARG A:421 , ARG A:455 , BME A:756 , HOH A:825 , HOH A:1144 , HOH A:1196 , HOH A:1222
BINDING SITE FOR RESIDUE SIN A 766
12
BC3
SOFTWARE
LYS A:94 , GLU A:96 , HOH A:973
BINDING SITE FOR RESIDUE GOL A 767
13
BC4
SOFTWARE
GLY A:622 , TYR A:623 , LYS A:624 , PHE A:671 , HOH A:1220
BINDING SITE FOR RESIDUE GOL A 768
14
BC5
SOFTWARE
ARG A:182 , ARG A:212 , TYR A:216 , ASN A:217 , GLY A:264 , GLU A:579 , HOH A:1229 , HOH A:1427
BINDING SITE FOR RESIDUE GOL A 769
15
BC6
SOFTWARE
ALA A:569 , VAL A:643 , GOL A:765 , GOL A:787 , HOH A:1113 , HOH A:1421
BINDING SITE FOR RESIDUE GOL A 770
16
BC7
SOFTWARE
PHE A:146 , GLY A:152 , ALA A:153 , TYR A:155 , SER A:228 , ARG A:246 , PRO A:664 , GLY A:665 , VAL A:666 , HOH A:808 , HOH A:1020
BINDING SITE FOR RESIDUE GOL A 771
17
BC8
SOFTWARE
ARG A:454 , ARG A:455 , TYR A:456 , THR A:457
BINDING SITE FOR RESIDUE GOL A 772
18
BC9
SOFTWARE
GLU A:84 , PHE A:85 , PRO A:117 , HOH A:1095 , HOH A:1383
BINDING SITE FOR RESIDUE GOL A 773
19
CC1
SOFTWARE
GLY A:301 , HOH A:814 , HOH A:1331
BINDING SITE FOR RESIDUE GOL A 774
20
CC2
SOFTWARE
ARG A:440 , LYS A:441 , GLU A:580 , PHE A:581 , ALA A:636 , TYR A:691 , HOH A:1139
BINDING SITE FOR RESIDUE GOL A 775
21
CC3
SOFTWARE
SER A:555 , HIS A:561 , HOH A:1257 , HOH A:1470
BINDING SITE FOR RESIDUE GOL A 776
22
CC4
SOFTWARE
TRP A:160 , GLU A:251 , LYS A:254 , TYR A:331 , GLU A:335
BINDING SITE FOR RESIDUE GOL A 777
23
CC5
SOFTWARE
LYS A:57 , PHE A:58 , ARG A:70 , ARG A:323
BINDING SITE FOR RESIDUE GOL A 778
24
CC6
SOFTWARE
VAL A:411
BINDING SITE FOR RESIDUE GOL A 779
25
CC7
SOFTWARE
TRP A:72 , PHE A:100 , HIS A:294 , GLU A:295 , EPE A:758 , HOH A:1096 , HOH A:1169 , HOH A:1467
BINDING SITE FOR RESIDUE GOL A 780
26
CC8
SOFTWARE
GLY A:189 , TYR A:200 , ALA A:223 , HIS A:227 , SER A:244 , ARG A:246 , SER A:247 , HOH A:940
BINDING SITE FOR RESIDUE GOL A 781
27
CC9
SOFTWARE
ARG A:649 , GLY A:651 , LEU A:681 , SIN A:789 , HOH A:1053 , HOH A:1329
BINDING SITE FOR RESIDUE GOL A 782
28
DC1
SOFTWARE
ASP A:15 , TRP A:88 , ARG A:125
BINDING SITE FOR RESIDUE GOL A 783
29
DC2
SOFTWARE
GLU A:196 , PRO A:630 , ASN A:676 , HOH A:855 , HOH A:1076 , HOH A:1450
BINDING SITE FOR RESIDUE GOL A 784
30
DC3
SOFTWARE
PRO A:74 , ALA A:75 , LYS A:97 , GLU A:295 , HOH A:1305
BINDING SITE FOR RESIDUE GOL A 785
31
DC4
SOFTWARE
LYS A:177 , PRO A:178 , ASP A:179 , PRO A:181 , PHE A:420 , LYS A:459 , HOH A:876 , HOH A:971 , HOH A:974 , HOH A:1428
BINDING SITE FOR RESIDUE GOL A 786
32
DC5
SOFTWARE
LYS A:565 , ASN A:568 , ALA A:569 , GLN A:572 , GOL A:770 , HOH A:1295
BINDING SITE FOR RESIDUE GOL A 787
33
DC6
SOFTWARE
ASP A:439 , PRO A:616 , ARG A:685 , HOH A:1075
BINDING SITE FOR RESIDUE GOL A 788
34
DC7
SOFTWARE
GLY A:622 , VAL A:654 , ASP A:655 , LYS A:679 , VAL A:680 , LEU A:681 , GOL A:782
BINDING SITE FOR RESIDUE SIN A 789
35
DC8
SOFTWARE
ASP A:98 , LYS A:99
BINDING SITE FOR RESIDUE GOL A 790
36
DC9
SOFTWARE
GLN A:494 , PRO A:495 , HOH A:1436
BINDING SITE FOR RESIDUE GOL A 791
37
EC1
SOFTWARE
SER A:228 , TYR A:229 , PRO A:667 , GLU A:668 , HOH A:808 , HOH A:1259
BINDING SITE FOR RESIDUE GOL A 792
38
EC2
SOFTWARE
LYS A:441 , GLU A:580
BINDING SITE FOR RESIDUE GOL A 793
[
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
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 (264 KB)
Header - Asym.Unit
Biol.Unit 1 (256 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
3AML
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help