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.
1R19
Biol. Unit 4
Info
Asym.Unit (163 KB)
Biol.Unit 1 (40 KB)
Biol.Unit 2 (42 KB)
Biol.Unit 3 (42 KB)
Biol.Unit 4 (41 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 ANALYSIS OF S.EPIDERMIDIS ADHESIN SDRG BINDING TO FIBRINOGEN (APO STRUCTURE)
Authors
:
K. Ponnuraj, M. G. Bowden, S. Davis, S. Gurusiddappa, D. Moore, D. Choe, Y. Xu, M. Hook, S. V. L. Narayana
Date
:
23 Sep 03 (Deposition) - 28 Oct 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.51
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Mscramm, Sdrg Native, Cell Adhesion
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Ponnuraj, M. G. Bowden, S. Davis, S. Gurusiddappa, D. Moore, D. Choe, Y. Xu, M. Hook, S. V. L. Narayana
A "Dock, Lock And Latch" Structural Model For A Staphylococcal Adhesin Binding To Fibrinogen
Cell(Cambridge, Mass. ) V. 115 217 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d1r19a1 (A:277-424)
1b: SCOP_d1r19b1 (B:277-424)
1c: SCOP_d1r19b2 (B:425-584)
1d: SCOP_d1r19c1 (C:277-424)
1e: SCOP_d1r19c2 (C:425-584)
1f: SCOP_d1r19d1 (D:277-424)
1g: SCOP_d1r19d2 (D:425-586)
1h: SCOP_d1r19a2 (A:425-580)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Common fold of diphtheria toxin/transcription factors/cytochrome f
(364)
Superfamily
:
Bacterial adhesins
(93)
Family
:
Fibrinogen-binding domain
(4)
Protein domain
:
Fibrinogen-binding adhesin SdrG
(3)
Staphylococcus epidermidis [TaxId: 1282]
(3)
1a
d1r19a1
A:277-424
1b
d1r19b1
B:277-424
1c
d1r19b2
B:425-584
1d
d1r19c1
C:277-424
1e
d1r19c2
C:425-584
1f
d1r19d1
D:277-424
1g
d1r19d2
D:425-586
1h
d1r19a2
A:425-580
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1r19B01 (B:277-424,B:583-584)
1b: CATH_1r19C01 (C:277-424,C:583-584)
1c: CATH_1r19D01 (D:277-424,D:583-586)
1d: CATH_1r19A01 (A:277-424)
2a: CATH_1r19B02 (B:425-582)
2b: CATH_1r19C02 (C:425-582)
2c: CATH_1r19D02 (D:425-582)
2d: CATH_1r19A02 (A:425-580)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.1280, no name defined]
(4)
Staphylococcus epidermidis. Organism_taxid: 1282.
(3)
1a
1r19B01
B:277-424,B:583-584
1b
1r19C01
C:277-424,C:583-584
1c
1r19D01
D:277-424,D:583-586
1d
1r19A01
A:277-424
Homologous Superfamily
:
[code=2.60.40.1290, no name defined]
(4)
Staphylococcus epidermidis. Organism_taxid: 1282.
(3)
2a
1r19B02
B:425-582
2b
1r19C02
C:425-582
2c
1r19D02
D:425-582
2d
1r19A02
A:425-580
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_SdrG_C_C_1r19D01 (D:425-583)
1b: PFAM_SdrG_C_C_1r19D02 (D:425-583)
1c: PFAM_SdrG_C_C_1r19D03 (D:425-583)
1d: PFAM_SdrG_C_C_1r19D04 (D:425-583)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: SdrG_C_C]
(5)
Family
:
SdrG_C_C
(5)
Staphylococcus epidermidis
(3)
1a
SdrG_C_C-1r19D01
D:425-583
1b
SdrG_C_C-1r19D02
D:425-583
1c
SdrG_C_C-1r19D03
D:425-583
1d
SdrG_C_C-1r19D04
D:425-583
[
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 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 (163 KB)
Header - Asym.Unit
Biol.Unit 1 (40 KB)
Header - Biol.Unit 1
Biol.Unit 2 (42 KB)
Header - Biol.Unit 2
Biol.Unit 3 (42 KB)
Header - Biol.Unit 3
Biol.Unit 4 (41 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
1R19
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
