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.
PLEASE WAIT...
Getting 'Exon' information from database.
4X7F
Asym. Unit
Info
Asym.Unit (288 KB)
Biol.Unit 1 (277 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 OF NOROVIRUS GII.10 P DOMAIN IN COMPLEX WITH NANO-25
Authors
:
A. D. Koromyslova, G. S. Hansman
Date
:
09 Dec 14 (Deposition) - 31 Dec 14 (Release) - 18 Feb 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Nanobody, Vhh Domain, Norovirus, Protruding Domain, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. D. Koromyslova, G. S. Hansman
Nanobody Binding To A Conserved Epitope Promotes Norovirus Particle Disassembly.
J. Virol. V. 89 2718 2015
[
close entry info
]
Hetero Components
(4, 27)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
1t: 1,2-ETHANEDIOL (EDOt)
1u: 1,2-ETHANEDIOL (EDOu)
1v: 1,2-ETHANEDIOL (EDOv)
1w: 1,2-ETHANEDIOL (EDOw)
2a: IMIDAZOLE (IMDa)
2b: IMIDAZOLE (IMDb)
3a: SODIUM ION (NAa)
4a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
23
Ligand/Ion
1,2-ETHANEDIOL
2
IMD
2
Ligand/Ion
IMIDAZOLE
3
NA
1
Ligand/Ion
SODIUM ION
4
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(27, 27)
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: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:269 , ARG A:501
binding site for residue NA A 601
02
AC2
SOFTWARE
ASN A:309 , LEU A:310 , ASN A:311 , HOH A:736 , HOH A:758 , HOH A:799
binding site for residue EDO A 602
03
AC3
SOFTWARE
LEU A:279 , THR A:281 , GLY A:282 , HOH A:741 , HOH A:748
binding site for residue EDO A 603
04
AC4
SOFTWARE
PHE A:408 , GLN A:410 , PRO A:455 , ALA A:456 , HOH A:774
binding site for residue EDO A 604
05
AC5
SOFTWARE
ARG A:341 , HOH A:742 , PHE B:445 , PRO B:447
binding site for residue EDO A 605
06
AC6
SOFTWARE
LEU A:272 , GLN A:273 , GLY A:274 , THR A:276 , LEU A:325 , HOH A:870
binding site for residue EDO A 606
07
AC7
SOFTWARE
GLN A:277 , LEU A:278 , GLU B:236 , HOH B:765
binding site for residue EDO A 607
08
AC8
SOFTWARE
VAL A:361 , SER A:379 , THR A:380
binding site for residue EDO A 608
09
AC9
SOFTWARE
THR A:233 , GLY A:235 , EDO B:605
binding site for residue EDO A 609
10
AD1
SOFTWARE
ASP A:247 , EDO B:604
binding site for residue EDO A 610
11
AD2
SOFTWARE
TYR A:470 , GLN A:471 , HIS C:114
binding site for residue EDO A 611
12
AD3
SOFTWARE
GLU A:236 , HOH A:812 , GLN B:277 , LEU B:278
binding site for residue EDO A 612
13
AD4
SOFTWARE
ASP A:316 , THR A:318 , LEU A:494 , PHE A:495 , VAL A:515 , VAL A:516 , HOH A:703 , HOH A:704
binding site for residue EDO A 613
14
AD5
SOFTWARE
ARG A:287 , ASN A:311 , HOH A:782 , PRO B:245 , ILE B:246 , ASP B:247 , HOH B:775
binding site for residue EDO A 614
15
AD6
SOFTWARE
HIS A:358 , GLU A:359 , GLU A:382 , HOH A:784 , HOH A:874 , GLU B:359 , LYS B:449
binding site for residue PO4 A 615
16
AD7
SOFTWARE
PHE B:408 , GLN B:410 , PRO B:455 , ALA B:456 , HOH B:741 , HOH B:791 , HOH B:889
binding site for residue EDO B 601
17
AD8
SOFTWARE
LEU B:234 , VAL B:248 , LEU B:249 , VAL B:515 , ALA B:517 , THR B:519 , HOH B:856
binding site for residue EDO B 602
18
AD9
SOFTWARE
LEU B:272 , GLN B:273 , GLY B:274 , THR B:276 , LEU B:325 , HOH B:837
binding site for residue EDO B 603
19
AE1
SOFTWARE
PHE A:445 , PRO A:447 , EDO A:610 , ARG B:341 , HOH B:772
binding site for residue EDO B 604
20
AE2
SOFTWARE
EDO A:609 , ASN B:309 , LEU B:310 , ASN B:311 , HOH B:739 , HOH B:807 , HOH B:810
binding site for residue EDO B 605
21
AE3
SOFTWARE
TYR B:470 , GLN B:471 , SER B:473 , HOH B:805
binding site for residue EDO B 606
22
AE4
SOFTWARE
THR B:318 , GLU B:319 , ASP B:320 , LYS B:372 , ASN B:425
binding site for residue EDO B 607
23
AE5
SOFTWARE
PRO A:245 , THR B:281 , GLY B:282 , LEU B:310 , LYS B:393 , HOH B:754 , HOH B:762 , HOH B:879
binding site for residue EDO B 608
24
AE6
SOFTWARE
PRO A:243 , PRO A:280 , HOH A:806 , PRO B:243 , PRO B:280 , THR B:281 , HOH B:756
binding site for residue IMD B 609
25
AE7
SOFTWARE
PHE A:434 , PRO A:435 , GLU C:46 , LEU C:47
binding site for residue EDO C 201
26
AE8
SOFTWARE
ASP A:479 , GLN A:531 , THR C:52 , SER C:56 , THR C:57 , HOH C:302
binding site for residue IMD C 202
27
AE9
SOFTWARE
ARG D:38 , GLU D:46 , ALA D:60 , SER D:62 , HOH D:328
binding site for residue EDO D 201
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 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.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 A
Chain B
Chain C
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 (288 KB)
Header - Asym.Unit
Biol.Unit 1 (277 KB)
Header - Biol.Unit 1
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
4X7F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help