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.
4LSV
Asym. Unit
Info
Asym.Unit (274 KB)
Biol.Unit 1 (265 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 BROADLY AND POTENTLY NEUTRALIZING ANTIBODY 3BNC117 IN COMPLEX WITH HIV-1 CLADE C C1086 GP120
Authors
:
T. Zhou, S. Moquin, P. D. Kwong
Date
:
23 Jul 13 (Deposition) - 21 Aug 13 (Release) - 07 May 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : G,H,L
Biol. Unit 1: G,H,L (1x)
Keywords
:
Neutralizing Antibody 3Bnc117, Viral Protein-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Zhou, J. Zhu, X. Wu, S. Moquin, B. Zhang, P. Acharya, I. S. Georgiev, H. R. Altae-Tran, G. Y. Chuang, M. G. Joyce, Y. Do Kwon, N. S. Longo, M. K. Louder, T. Luongo, K. Mckee, C. A. Schramm, J. Skinner, Y. Yang, Z. Yang, Z. Zhang, A. Zheng, M. Bonsignori, B. F. Haynes, J. F. Scheid, M. C. Nussenzweig, M. Simek, D. R. Burton, W. C. Koff, J. C. Mullikin, M. Connors, L. Shapiro, G. J. Nabel, J. R. Mascola, P. D. Kwong
Multidonor Analysis Reveals Structural Elements, Genetic Determinants, And Maturation Pathway For Hiv-1 Neutralization By Vrc01-Class Antibodies.
Immunity V. 39 245 2013
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: IMIDAZOLE (IMDa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IMD
1
Ligand/Ion
IMIDAZOLE
2
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(12, 12)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN L:37 , LYS L:45 , PRO L:59 , GLU L:81 , ASP L:82
BINDING SITE FOR RESIDUE IMD L 302
02
AC2
SOFTWARE
ASN G:234 , THR G:236 , ILE G:272 , SER G:274
BINDING SITE FOR MONO-SACCHARIDE NAG G 501 BOUND TO ASN G 234
03
AC3
SOFTWARE
ASN G:229 , ASN G:241
BINDING SITE FOR MONO-SACCHARIDE NAG G 502 BOUND TO ASN G 241
04
AC4
SOFTWARE
LYS G:252 , ASN G:262 , ASN G:446 , SER G:447
BINDING SITE FOR MONO-SACCHARIDE NAG G 503 BOUND TO ASN G 262
05
AC5
SOFTWARE
GLU G:275 , ASN G:276 , GLY L:27 , TYR L:32 , TYR L:91
BINDING SITE FOR MONO-SACCHARIDE NAG G 504 BOUND TO ASN G 276
06
AC6
SOFTWARE
ASN G:289 , GLU G:290 , LYS G:344 , HOH G:625 , ALA L:184
BINDING SITE FOR MONO-SACCHARIDE NAG G 505 BOUND TO ASN G 289
07
AC7
SOFTWARE
ASN G:339 , ASN G:340 , GLN G:343 , SER L:127
BINDING SITE FOR MONO-SACCHARIDE NAG G 506 BOUND TO ASN G 339
08
AC8
SOFTWARE
ASN G:386 , SER G:388 , ARG H:19
BINDING SITE FOR MONO-SACCHARIDE NAG G 507 BOUND TO ASN G 386
09
AC9
SOFTWARE
PRO G:363 , ASP G:389 , ASN G:392 , THR G:406 , ARG G:408 , THR H:12 , SER H:17
BINDING SITE FOR MONO-SACCHARIDE NAG G 508 BOUND TO ASN G 392
10
BC1
SOFTWARE
ARG G:396 , ASN G:397
BINDING SITE FOR MONO-SACCHARIDE NAG G 509 BOUND TO ASN G 397
11
BC2
SOFTWARE
SER G:291 , ASN G:446 , ASN G:448
BINDING SITE FOR MONO-SACCHARIDE NAG G 510 BOUND TO ASN G 448
12
BC3
SOFTWARE
SER L:10 , THR L:20 , ARG L:65 , GLU L:70 , ASN L:72 , GLN L:199 , HOH L:403
BINDING SITE FOR MONO-SACCHARIDE NAG L 301 BOUND TO ASN L 72
[
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 (274 KB)
Header - Asym.Unit
Biol.Unit 1 (265 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
4LSV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help