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.
1R8H
Biol. Unit 1
Info
Asym.Unit (111 KB)
Biol.Unit 1 (35 KB)
Biol.Unit 2 (35 KB)
Biol.Unit 3 (39 KB)
Biol.Unit 4 (105 KB)
Biol.Unit 5 (36 KB)
Biol.Unit 6 (37 KB)
Biol.Unit 7 (37 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
COMPARISON OF THE STRUCTURE AND DNA BINDING PROPERTIES OF THE E2 PROTEINS FROM AN ONCOGENIC AND A NON-ONCOGENIC HUMAN PAPILLOMAVIRUS
Authors
:
G. Dell, K. W. Wilkinson, R. Tranter, J. Parish, R. L. Brady, K. Gaston
Date
:
24 Oct 03 (Deposition) - 23 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,E (1x)
Biol. Unit 3: C,F (1x)
Biol. Unit 4: A,B,C,D,E,F (1x)
Biol. Unit 5: A,B (1x)
Biol. Unit 6: E,F (1x)
Biol. Unit 7: C,D (1x)
Keywords
:
Anti-Parallel Beta-Barrel, Dna-Binding Domain, Transcription, Replication
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Dell, K. W. Wilkinson, R. Tranter, J. Parish, R. Leo Brady, K. Gaston
Comparison Of The Structure And Dna-Binding Properties Of The E2 Proteins From An Oncogenic And A Non-Oncogenic Human Papillomavirus.
J. Mol. Biol. V. 334 979 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 5)
Info
All Hetero Components
1a: PHOSPHATE ION (PO4a)
1b: PHOSPHATE ION (PO4b)
1c: PHOSPHATE ION (PO4c)
1d: PHOSPHATE ION (PO4d)
1e: PHOSPHATE ION (PO4e)
1f: PHOSPHATE ION (PO4f)
1g: PHOSPHATE ION (PO4g)
1h: PHOSPHATE ION (PO4h)
1i: PHOSPHATE ION (PO4i)
1j: PHOSPHATE ION (PO4j)
1k: PHOSPHATE ION (PO4k)
1l: PHOSPHATE ION (PO4l)
1m: PHOSPHATE ION (PO4m)
1n: PHOSPHATE ION (PO4n)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PO4
5
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC8 (SOFTWARE)
5: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS D:318 , SER D:321 , LYS D:327
BINDING SITE FOR RESIDUE PO4 D 501
2
AC3
SOFTWARE
ARG D:302 , HIS D:306 , LYS D:349 , HOH D:528 , HOH D:531
BINDING SITE FOR RESIDUE PO4 D 503
3
AC4
SOFTWARE
SER D:315 , THR D:316 , HOH D:544
BINDING SITE FOR RESIDUE PO4 D 504
4
AC8
SOFTWARE
ARG A:302 , HIS A:306 , LYS A:349 , HOH A:569
BINDING SITE FOR RESIDUE PO4 A 508
5
BC1
SOFTWARE
ARG A:300 , SER A:315 , THR A:316 , HOH A:563
BINDING SITE FOR RESIDUE PO4 A 510
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d1r8ha_ (A:)
1b: SCOP_d1r8hb_ (B:)
1c: SCOP_d1r8hc_ (C:)
1d: SCOP_d1r8hd_ (D:)
1e: SCOP_d1r8he_ (E:)
1f: SCOP_d1r8hf_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
Viral DNA-binding domain
(18)
Family
:
Viral DNA-binding domain
(18)
Protein domain
:
Papillomavirus-1 E2 protein
(16)
Human papillomavirus type 6a [TaxId: 37122]
(4)
1a
d1r8ha_
A:
1b
d1r8hb_
B:
1c
d1r8hc_
C:
1d
d1r8hd_
D:
1e
d1r8he_
E:
1f
d1r8hf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1r8hA00 (A:281-366)
1b: CATH_1r8hB00 (B:281-366)
1c: CATH_1r8hD00 (D:281-366)
1d: CATH_1r8hE00 (E:281-366)
1e: CATH_1r8hC00 (C:281-366)
1f: CATH_1r8hF00 (F:281-366)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.330, no name defined]
(307)
Human papillomavirus type 6a. Organism_taxid: 37122.
(2)
1a
1r8hA00
A:281-366
1b
1r8hB00
B:281-366
1c
1r8hD00
D:281-366
1d
1r8hE00
E:281-366
1e
1r8hC00
C:281-366
1f
1r8hF00
F:281-366
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PPV_E2_C_1r8hF01 (F:285-362)
1b: PFAM_PPV_E2_C_1r8hF02 (F:285-362)
1c: PFAM_PPV_E2_C_1r8hF03 (F:285-362)
1d: PFAM_PPV_E2_C_1r8hF04 (F:285-362)
1e: PFAM_PPV_E2_C_1r8hF05 (F:285-362)
1f: PFAM_PPV_E2_C_1r8hF06 (F:285-362)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: PPV_E2_C]
(7)
Family
:
PPV_E2_C
(7)
Human papillomavirus type 6a
(1)
1a
PPV_E2_C-1r8hF01
F:285-362
1b
PPV_E2_C-1r8hF02
F:285-362
1c
PPV_E2_C-1r8hF03
F:285-362
1d
PPV_E2_C-1r8hF04
F:285-362
1e
PPV_E2_C-1r8hF05
F:285-362
1f
PPV_E2_C-1r8hF06
F:285-362
[
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
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 (111 KB)
Header - Asym.Unit
Biol.Unit 1 (35 KB)
Header - Biol.Unit 1
Biol.Unit 2 (35 KB)
Header - Biol.Unit 2
Biol.Unit 3 (39 KB)
Header - Biol.Unit 3
Biol.Unit 4 (105 KB)
Header - Biol.Unit 4
Biol.Unit 5 (36 KB)
Header - Biol.Unit 5
Biol.Unit 6 (37 KB)
Header - Biol.Unit 6
Biol.Unit 7 (37 KB)
Header - Biol.Unit 7
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
1R8H
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help