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.
2ONK
Biol. Unit 2
Info
Asym.Unit (386 KB)
Biol.Unit 1 (192 KB)
Biol.Unit 2 (192 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ABC TRANSPORTER MODBC IN COMPLEX WITH ITS BINDING PROTEIN MODA
Authors
:
K. Hollenstein, D. C. Frei, K. P. Locher
Date
:
24 Jan 07 (Deposition) - 06 Mar 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F,G,H,I,J (1x)
Keywords
:
Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Hollenstein, D. C. Frei, K. P. Locher
Structure Of An Abc Transporter In Complex With Its Binding Protein.
Nature V. 446 213 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
3a: TUNGSTATE(VI)ION (WO4a)
3b: TUNGSTATE(VI)ION (WO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
PO4
2
Ligand/Ion
PHOSPHATE ION
3
WO4
1
Ligand/Ion
TUNGSTATE(VI)ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC1 (SOFTWARE)
6: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ALA J:40 , GLY J:41 , SER J:42 , GLY J:69 , SER J:70 , ALA J:90 , ASP J:153 , PRO J:154 , CYS J:155 , GLU J:218 , TYR J:236
BINDING SITE FOR RESIDUE WO4 J 702
2
AC5
SOFTWARE
PRO F:32 , GLY F:34 , ALA F:35 , GLY F:36 , LYS F:37 , SER F:38 , MG F:703
BINDING SITE FOR RESIDUE PO4 F 803
3
AC6
SOFTWARE
PRO G:32 , GLY G:34 , ALA G:35 , GLY G:36 , LYS G:37 , SER G:38 , MG G:704
BINDING SITE FOR RESIDUE PO4 G 804
4
AC9
SOFTWARE
SER F:38 , GLN F:77 , ASP F:151 , PO4 F:803
BINDING SITE FOR RESIDUE MG F 703
5
BC1
SOFTWARE
SER G:38 , GLN G:77 , ASP G:151 , PO4 G:804
BINDING SITE FOR RESIDUE MG G 704
6
BC3
SOFTWARE
GLU J:167 , PRO J:173 , ASP J:177
BINDING SITE FOR RESIDUE MG J 706
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ABC_TM1 (H:51-247,I:51-247)
2: ABC_TRANSPORTER_1 (F:127-141,G:127-141)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ABC_TM1
PS50928
ABC transporter integral membrane type-1 domain profile.
WTPB_ARCFU
51-247
2
-
-
H:51-247
I:51-247
2
ABC_TRANSPORTER_1
PS00211
ABC transporters family signature.
WTPC_ARCFU
127-141
2
-
-
F:127-141
G:127-141
[
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
(4, 10)
Info
All SCOP Domains
1a: SCOP_d2onkb_ (B:)
1b: SCOP_d2onkf_ (F:)
1c: SCOP_d2onkg_ (G:)
2a: SCOP_d2onka1 (A:1-240)
3a: SCOP_d2onke1 (E:32-342)
3b: SCOP_d2onkj_ (J:)
4a: SCOP_d2onkc1 (C:1-252)
4b: SCOP_d2onkd1 (D:1-252)
4c: SCOP_d2onkh1 (H:1-252)
4d: SCOP_d2onki1 (I:1-252)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
ABC transporter ATPase domain-like
(94)
Protein domain
:
automated matches
(8)
Archaeoglobus fulgidus [TaxId: 2234]
(1)
1a
d2onkb_
B:
1b
d2onkf_
F:
1c
d2onkg_
G:
Protein domain
:
Molybdate/tungstate import ATP-binding protein WtpC (ModC)
(1)
Archaeoglobus fulgidus [TaxId: 2234]
(1)
2a
d2onka1
A:1-240
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
Molybdate-binding protein, ModA
(6)
Archaeoglobus fulgidus [TaxId: 2234]
(3)
3a
d2onke1
E:32-342
3b
d2onkj_
J:
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
MetI-like
(24)
Superfamily
:
MetI-like
(24)
Family
:
MetI-like
(24)
Protein domain
:
Molybdate/tungstate transport system permease protein WtpB (ModB)
(1)
Archaeoglobus fulgidus [TaxId: 2234]
(1)
4a
d2onkc1
C:1-252
4b
d2onkd1
D:1-252
4c
d2onkh1
H:1-252
4d
d2onki1
I:1-252
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_2onkE01 (E:32-112,E:284-342)
1b: CATH_2onkJ01 (J:29-112,J:284-338)
1c: CATH_2onkE02 (E:113-283)
1d: CATH_2onkJ02 (J:113-283)
2a: CATH_2onkA00 (A:1-240)
2b: CATH_2onkB00 (B:1-240)
2c: CATH_2onkF00 (F:1-240)
2d: CATH_2onkG00 (G:1-240)
3a: CATH_2onkC00 (C:1-252)
3b: CATH_2onkD00 (D:1-252)
3c: CATH_2onkH00 (H:1-252)
3d: CATH_2onkI00 (I:1-252)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
D-Maltodextrin-Binding Protein; domain 2
(600)
Homologous Superfamily
:
Periplasmic binding protein-like II
(486)
Archaeoglobus fulgidus. Organism_taxid: 2234.
(1)
1a
2onkE01
E:32-112,E:284-342
1b
2onkJ01
J:29-112,J:284-338
1c
2onkE02
E:113-283
1d
2onkJ02
J:113-283
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Archaeoglobus fulgidus. Organism_taxid: 2234.
(4)
2a
2onkA00
A:1-240
2b
2onkB00
B:1-240
2c
2onkF00
F:1-240
2d
2onkG00
G:1-240
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
MetI-like fold
(4)
Homologous Superfamily
:
MetI-like domain
(4)
Archaeoglobus fulgidus. Organism_taxid: 2234.
(1)
3a
2onkC00
C:1-252
3b
2onkD00
D:1-252
3c
2onkH00
H:1-252
3d
2onkI00
I:1-252
[
close CATH info
]
Pfam Domains
(3, 10)
Info
all PFAM domains
1a: PFAM_BPD_transp_1_2onkI01 (I:69-252)
1b: PFAM_BPD_transp_1_2onkI02 (I:69-252)
1c: PFAM_BPD_transp_1_2onkI03 (I:69-252)
1d: PFAM_BPD_transp_1_2onkI04 (I:69-252)
2a: PFAM_ABC_tran_2onkG01 (G:38-155)
2b: PFAM_ABC_tran_2onkG02 (G:38-155)
2c: PFAM_ABC_tran_2onkG03 (G:38-155)
2d: PFAM_ABC_tran_2onkG04 (G:38-155)
3a: PFAM_SBP_bac_1_2onkJ01 (J:40-313)
3b: PFAM_SBP_bac_1_2onkJ02 (J:40-313)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
BPD_transp_1
(5)
Family
:
BPD_transp_1
(5)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
(1)
1a
BPD_transp_1-2onkI01
I:69-252
1b
BPD_transp_1-2onkI02
I:69-252
1c
BPD_transp_1-2onkI03
I:69-252
1d
BPD_transp_1-2onkI04
I:69-252
Clan
:
P-loop_NTPase
(1112)
Family
:
ABC_tran
(53)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
(1)
2a
ABC_tran-2onkG01
G:38-155
2b
ABC_tran-2onkG02
G:38-155
2c
ABC_tran-2onkG03
G:38-155
2d
ABC_tran-2onkG04
G:38-155
Clan
:
PBP
(391)
Family
:
SBP_bac_1
(83)
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
(3)
3a
SBP_bac_1-2onkJ01
J:40-313
3b
SBP_bac_1-2onkJ02
J:40-313
[
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 F
Chain G
Chain H
Chain I
Chain J
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 (386 KB)
Header - Asym.Unit
Biol.Unit 1 (192 KB)
Header - Biol.Unit 1
Biol.Unit 2 (192 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
2ONK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help