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.
4POQ
Biol. Unit 2
Info
Asym.Unit (899 KB)
Biol.Unit 1 (447 KB)
Biol.Unit 2 (446 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 UNLIGANDED VP1 PENTAMER OF HUMAN POLYOMAVIRUS 9
Authors
:
Z. M. Khan, T. Stehle
Date
:
26 Feb 14 (Deposition) - 09 Apr 14 (Release) - 26 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
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
:
Jelly Roll Fold, Capsid Formation, Receptor Interaction, Carbohydrate, Sialyloligosaccharide, Viral Coat Protein, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. M. Khan, Y. Liu, U. Neu, M. Gilbert, B. Ehlers, T. Feizi, T. Stehle
Crystallographic And Glycan Microarray Analysis Of Human Polyomavirus 9 Vp1 Identifies N-Glycolyl Neuraminic Acid As A Receptor Candidate.
J. Virol. V. 88 6100 2014
[
close entry info
]
Hetero Components
(2, 11)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
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)
3a: ISOPROPYL ALCOHOL (IPAa)
3b: ISOPROPYL ALCOHOL (IPAb)
3c: ISOPROPYL ALCOHOL (IPAc)
3d: ISOPROPYL ALCOHOL (IPAd)
3e: ISOPROPYL ALCOHOL (IPAe)
3f: ISOPROPYL ALCOHOL (IPAf)
3g: ISOPROPYL ALCOHOL (IPAg)
3h: ISOPROPYL ALCOHOL (IPAh)
3i: ISOPROPYL ALCOHOL (IPAi)
3j: ISOPROPYL ALCOHOL (IPAj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
IPA
5
Ligand/Ion
ISOPROPYL ALCOHOL
[
close Hetero Component info
]
Sites
(16, 16)
Info
All Sites
01: BC7 (SOFTWARE)
02: BC8 (SOFTWARE)
03: BC9 (SOFTWARE)
04: CC1 (SOFTWARE)
05: CC2 (SOFTWARE)
06: CC3 (SOFTWARE)
07: CC4 (SOFTWARE)
08: CC5 (SOFTWARE)
09: CC6 (SOFTWARE)
10: CC7 (SOFTWARE)
11: CC8 (SOFTWARE)
12: CC9 (SOFTWARE)
13: DC1 (SOFTWARE)
14: DC2 (SOFTWARE)
15: DC3 (SOFTWARE)
16: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC7
SOFTWARE
GLU F:49 , HOH F:637 , HOH F:638 , SER G:217 , GLU G:220 , HOH G:659
BINDING SITE FOR RESIDUE CA F 401
02
BC8
SOFTWARE
MET F:238 , GLN F:239 , HOH F:578
BINDING SITE FOR RESIDUE EDO F 402
03
BC9
SOFTWARE
ARG F:223 , TYR F:225 , VAL F:247 , LEU F:248 , LEU F:249 , HOH F:633 , SER J:243
BINDING SITE FOR RESIDUE EDO F 403
04
CC1
SOFTWARE
PHE F:156 , TYR F:225 , SER F:227
BINDING SITE FOR RESIDUE IPA F 404
05
CC2
SOFTWARE
GLU G:49 , SER H:217 , HOH H:681 , HOH H:682
BINDING SITE FOR RESIDUE CA G 401
06
CC3
SOFTWARE
VAL G:33 , HOH G:616 , HOH G:633
BINDING SITE FOR RESIDUE EDO G 402
07
CC4
SOFTWARE
VAL G:122 , HIS G:154 , MET G:238 , GLN G:239 , HOH G:529 , HOH G:614
BINDING SITE FOR RESIDUE EDO G 403
08
CC5
SOFTWARE
HIS G:154 , PHE G:156 , TYR G:225 , HOH G:529
BINDING SITE FOR RESIDUE IPA G 404
09
CC6
SOFTWARE
GLU H:49 , SER I:217 , GLU I:220 , HOH I:634 , HOH I:652 , HOH I:656
BINDING SITE FOR RESIDUE CA H 401
10
CC7
SOFTWARE
HIS H:154 , PHE H:156 , SER H:227 , HOH H:542
BINDING SITE FOR RESIDUE IPA H 402
11
CC8
SOFTWARE
GLU I:49 , HOH I:664 , SER J:217 , HOH J:562 , HOH J:650 , HOH J:656
BINDING SITE FOR RESIDUE CA I 401
12
CC9
SOFTWARE
MET I:238 , GLN I:239 , HOH I:590 , HOH I:645
BINDING SITE FOR RESIDUE EDO I 402
13
DC1
SOFTWARE
HIS I:154 , TYR I:225 , GLY I:226 , SER I:227 , HOH I:645
BINDING SITE FOR RESIDUE IPA I 403
14
DC2
SOFTWARE
SER F:217 , HOH F:642 , HOH F:649 , GLU J:49
BINDING SITE FOR RESIDUE CA J 401
15
DC3
SOFTWARE
MET J:238 , GLN J:239 , HOH J:655
BINDING SITE FOR RESIDUE EDO J 402
16
DC4
SOFTWARE
PHE J:156 , SER J:227 , ARG J:288
BINDING SITE FOR RESIDUE IPA J 403
[
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, 10)
Info
All SCOP Domains
1a: SCOP_d4poqa_ (A:)
1b: SCOP_d4poqb_ (B:)
1c: SCOP_d4poqc_ (C:)
1d: SCOP_d4poqd_ (D:)
1e: SCOP_d4poqe_ (E:)
1f: SCOP_d4poqf_ (F:)
1g: SCOP_d4poqg_ (G:)
1h: SCOP_d4poqh_ (H:)
1i: SCOP_d4poqi_ (I:)
1j: SCOP_d4poqj_ (J:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Nucleoplasmin-like/VP (viral coat and capsid proteins)
(278)
Superfamily
:
Group I dsDNA viruses
(30)
Family
:
Papovaviridae-like VP
(19)
Protein domain
:
automated matches
(12)
Human polyomavirus 9 [TaxId: 943908]
(7)
1a
d4poqa_
A:
1b
d4poqb_
B:
1c
d4poqc_
C:
1d
d4poqd_
D:
1e
d4poqe_
E:
1f
d4poqf_
F:
1g
d4poqg_
G:
1h
d4poqh_
H:
1i
d4poqi_
I:
1j
d4poqj_
J:
[
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 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 (899 KB)
Header - Asym.Unit
Biol.Unit 1 (447 KB)
Header - Biol.Unit 1
Biol.Unit 2 (446 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
4POQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
