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.
3CK9
Biol. Unit 1
Info
Asym.Unit (190 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (93 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
B. THETAIOTAOMICRON SUSD WITH MALTOHEPTAOSE
Authors
:
N. M. Koropatkin, E. C. Martens, J. I. Gordon, T. J. Smith
Date
:
14 Mar 08 (Deposition) - 20 May 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Tpr Repeat, Carbohydrate Binding, Starch Binding, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. M. Koropatkin, E. C. Martens, J. I. Gordon, T. J. Smith
Starch Catabolism By A Prominent Human Gut Symbiont Is Directed By The Recognition Of Amylose Helices.
Structure V. 16 1105 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
3a: ALPHA-D-GLUCOSE (GLCa)
3b: ALPHA-D-GLUCOSE (GLCb)
3c: ALPHA-D-GLUCOSE (GLCc)
3d: ALPHA-D-GLUCOSE (GLCd)
3e: ALPHA-D-GLUCOSE (GLCe)
3f: ALPHA-D-GLUCOSE (GLCf)
3g: ALPHA-D-GLUCOSE (GLCg)
3h: ALPHA-D-GLUCOSE (GLCh)
3i: ALPHA-D-GLUCOSE (GLCi)
3j: ALPHA-D-GLUCOSE (GLCj)
3k: ALPHA-D-GLUCOSE (GLCk)
3l: ALPHA-D-GLUCOSE (GLCl)
3m: ALPHA-D-GLUCOSE (GLCm)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
3
GLC
7
Ligand/Ion
ALPHA-D-GLUCOSE
[
close Hetero Component info
]
Sites
(19, 19)
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: BC2 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC9 (SOFTWARE)
13: CC1 (SOFTWARE)
14: CC2 (SOFTWARE)
15: CC3 (SOFTWARE)
16: CC4 (SOFTWARE)
17: CC5 (SOFTWARE)
18: CC7 (SOFTWARE)
19: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:73 , GLC A:802 , GLC A:807 , HOH A:947 , TRP B:224 , LYS B:252 , GLY B:255 , SER B:256
BINDING SITE FOR RESIDUE GLC A 801
02
AC2
SOFTWARE
GLC A:801 , GLC A:803 , GLU B:209 , TRP B:224 , LYS B:252 , HOH B:1015
BINDING SITE FOR RESIDUE GLC A 802
03
AC3
SOFTWARE
GLC A:802 , GLC A:804 , HOH A:1023 , GLU B:209 , HOH B:1015
BINDING SITE FOR RESIDUE GLC A 803
04
AC4
SOFTWARE
TRP A:98 , GLC A:803 , GLC A:805 , HOH A:1010
BINDING SITE FOR RESIDUE GLC A 804
05
AC5
SOFTWARE
TRP A:96 , TRP A:98 , ASN A:101 , TRP A:320 , SER A:321 , CYS A:322 , GLC A:804 , GLC A:806 , HOH A:946
BINDING SITE FOR RESIDUE GLC A 805
06
AC6
SOFTWARE
ARG A:81 , TYR A:296 , TRP A:320 , GLC A:805 , GLC A:807 , HOH A:1041 , HOH A:1064 , HOH A:1091
BINDING SITE FOR RESIDUE GLC A 806
07
AC7
SOFTWARE
ASP A:73 , GLU A:74 , GLY A:75 , GLC A:801 , GLC A:806 , HOH A:987
BINDING SITE FOR RESIDUE GLC A 807
08
BC2
SOFTWARE
ARG A:451 , HOH A:983 , TRP B:98 , GLC B:903 , GLC B:905 , HOH B:1029 , HOH B:1101 , HOH B:1133
BINDING SITE FOR RESIDUE GLC B 904
09
BC3
SOFTWARE
THR A:241 , TYR A:243 , ARG A:451 , HOH A:968 , GLC B:904 , GLC B:906
BINDING SITE FOR RESIDUE GLC B 905
10
BC5
SOFTWARE
ASP A:273 , GLN A:288 , ASP A:430 , ASP A:432 , HOH A:1134 , HOH A:1208 , HOH A:1214
BINDING SITE FOR RESIDUE CA A 600
11
BC6
SOFTWARE
GLU A:274 , EDO A:731 , HOH A:984 , HOH A:992 , HOH A:1031
BINDING SITE FOR RESIDUE CA A 710
12
BC9
SOFTWARE
TYR A:52 , GLY A:216 , HOH A:988 , HOH A:1076
BINDING SITE FOR RESIDUE EDO A 730
13
CC1
SOFTWARE
GLU A:274 , ARG A:417 , PRO A:422 , ASP A:430 , CA A:710 , HOH A:1135 , HOH A:1207 , GLY B:40 , EDO B:734
BINDING SITE FOR RESIDUE EDO A 731
14
CC2
SOFTWARE
GLN A:331 , GLN A:397 , TRP A:512 , ASP A:513
BINDING SITE FOR RESIDUE EDO A 736
15
CC3
SOFTWARE
GLY A:127 , THR A:131 , PRO A:174 , LYS A:176 , HOH A:1039
BINDING SITE FOR RESIDUE EDO A 737
16
CC4
SOFTWARE
ARG A:211 , PHE A:215 , MET A:279 , HOH A:847 , HOH A:991
BINDING SITE FOR RESIDUE EDO A 747
17
CC5
SOFTWARE
PHE A:450 , EDO B:733
BINDING SITE FOR RESIDUE EDO B 732
18
CC7
SOFTWARE
ASP A:289 , VAL A:291 , LYS A:292 , SER A:424 , EDO A:731 , GLY B:40 , PHE B:42 , HOH B:977
BINDING SITE FOR RESIDUE EDO B 734
19
DC1
SOFTWARE
GLY A:40 , PHE A:42 , ASP B:289 , VAL B:291 , LYS B:292 , HOH B:979
BINDING SITE FOR RESIDUE EDO B 744
[
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ck9a_ (A:)
1b: SCOP_d3ck9b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha-alpha superhelix
(690)
Superfamily
:
TPR-like
(83)
Family
:
SusD-like
(7)
Protein domain
:
Starch utilization system protein SusD
(5)
Bacteroides thetaiotaomicron [TaxId: 818]
(5)
1a
d3ck9a_
A:
1b
d3ck9b_
B:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3ck9A02 (A:210-307,A:412-490)
1b: CATH_3ck9B02 (B:210-307,B:412-490)
2a: CATH_3ck9A03 (A:308-411)
2b: CATH_3ck9B03 (B:308-411)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Alpha Horseshoe
(399)
Topology
:
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
(320)
Homologous Superfamily
:
[code=1.25.40.10, no name defined]
(42)
Bacteroides thetaiotaomicron. Strain: vpi-5482.
(1)
1a
3ck9A02
A:210-307,A:412-490
1b
3ck9B02
B:210-307,B:412-490
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
TPR-like
(5)
Homologous Superfamily
:
SusD-like
(5)
Bacteroides thetaiotaomicron. Strain: vpi-5482.
(1)
2a
3ck9A03
A:308-411
2b
3ck9B03
B:308-411
[
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 (190 KB)
Header - Asym.Unit
Biol.Unit 1 (94 KB)
Header - Biol.Unit 1
Biol.Unit 2 (93 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
3CK9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
