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.
4OLU
Asym. Unit
Info
Asym.Unit (273 KB)
Biol.Unit 1 (266 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 ANTIBODY VRC07 IN COMPLEX WITH CLADE A/E 93TH057 HIV-1 GP120 CORE
Authors
:
Y. D. Kwon, P. D. Kwong
Date
:
25 Jan 14 (Deposition) - 03 Sep 14 (Release) - 22 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : G,H,L
Biol. Unit 1: G,H,L (1x)
Keywords
:
Vrc07 Antibody, Passive Transfer, Neutralization, In Vivo Protection, Autoreactivity, Lentiviral Infection, Enhanced Potency, Hiv-1 Gp120, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. S. Rudicell, Y. D. Kwon, S. Y. Ko, A. Pegu, M. K. Louder, I. S. Georgiev X. Wu, J. Zhu, J. C. Boyington, X. Chen, W. Shi, Z. Y. Yang, N. A. Doria-Rose, K. Mckee, S. O'Dell, S. D. Schmidt, G. Y. Chuang, A. Druz, C. Soto, Y. Yang, B. Zhang, T. Zhou, J. P. Todd, K. E. Lloyd, J. Eudailey, K. E. Roberts, B. R. Donald, R. T. Bailer, J. Ledgerwood, J. C. Mullikin, L. Shapiro, R. A. Koup, B. S. Graham, M. C. Nason, M. Connors, B. F. Haynes, S. S. Rao, M. Roederer, P. D. Kwong, J. R. Mascola, G. J. Nabel
Enhanced Potency Of A Broadly Neutralizing Hiv-1 Antibody I Vitro Improves Protection Against Lentiviral Infection In Vivo.
J. Virol. V. 88 12669 2014
[
close entry info
]
Hetero Components
(1, 10)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(10, 10)
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: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN G:234 , PRO G:238 , HIS G:352 , HOH G:614 , HOH G:626 , HOH G:719 , GLN H:192
BINDING SITE FOR RESIDUE NAG G 501
02
AC2
SOFTWARE
ASP G:230 , LYS G:231 , ASN G:232 , ASN G:241
BINDING SITE FOR RESIDUE NAG G 502
03
AC3
SOFTWARE
ASN G:262 , ARG G:379 , CYS G:445 , VAL G:446 , SER G:447 , HOH G:604 , HOH G:620 , HOH G:625
BINDING SITE FOR RESIDUE NAG G 503
04
AC4
SOFTWARE
GLU G:275 , ASN G:276 , HOH G:705 , SER L:30 , TYR L:91
BINDING SITE FOR RESIDUE NAG G 504
05
AC5
SOFTWARE
GLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLN G:344
BINDING SITE FOR RESIDUE NAG G 505
06
AC6
SOFTWARE
ASN G:295 , THR G:297 , TYR G:330 , GLU G:332
BINDING SITE FOR RESIDUE NAG G 506
07
AC7
SOFTWARE
ASN G:334 , LYS G:337 , THR G:413
BINDING SITE FOR RESIDUE NAG G 507
08
AC8
SOFTWARE
GLN G:117 , GLN G:203 , ASN G:386 , THR G:388
BINDING SITE FOR RESIDUE NAG G 508
09
AC9
SOFTWARE
THR G:388 , GLN G:389 , ASN G:392 , GLY G:409 , CYS G:410 , HOH G:693
BINDING SITE FOR RESIDUE NAG G 509
10
BC1
SOFTWARE
SER G:291 , ASN G:448 , HOH G:673
BINDING SITE FOR RESIDUE NAG G 510
[
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 G
Chain H
Chain L
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 (273 KB)
Header - Asym.Unit
Biol.Unit 1 (266 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
4OLU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
