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.
1RZG
Asym. Unit
Info
Asym.Unit (157 KB)
Biol.Unit 1 (79 KB)
Biol.Unit 2 (76 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 HUMAN ANTI-HIV-1 GP120 REACTIVE ANTIBODY 412D
Authors
:
C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, H. Choe, M. Farzan, P. D. Kwong
Date
:
24 Dec 03 (Deposition) - 03 Feb 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Hiv-1; Gp120; Cd4I; Antibodies; Tyrosine Sulfation; Vh-Gene Usage, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. C. Huang, M. Venturi, S. Majeed, M. J. Moore, S. Phogat, M. -Y. Zhang, D. S. Dimitrov, W. A. Hendrickson, J. Robinson, J. Sodroski, R. Wyatt, H. Choe, M. Farzan, P. D. Kwong
Structural Basis Of Tyrosine Sulfation And Vh-Gene Usage In Antibodies That Recognize The Hiv Type 1 Coreceptor-Binding Site On Gp120
Proc. Natl. Acad. Sci. Usa V. 101 2706 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 11)
Info
All Hetero Components
1a: ASPARTIC ACID (ASPa)
2a: CYSTEINE (CYSa)
3a: SUCROSE (SUCa)
3b: SUCROSE (SUCb)
3c: SUCROSE (SUCc)
3d: SUCROSE (SUCd)
3e: SUCROSE (SUCe)
3f: SUCROSE (SUCf)
3g: SUCROSE (SUCg)
4a: O-SULFO-L-TYROSINE (TYSa)
4b: O-SULFO-L-TYROSINE (TYSb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ASP
1
Mod. Amino Acid
ASPARTIC ACID
2
CYS
1
Mod. Amino Acid
CYSTEINE
3
SUC
7
Ligand/Ion
SUCROSE
4
TYS
2
Mod. Amino Acid
O-SULFO-L-TYROSINE
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:59 , GLN A:64 , GLY A:65 , ARG A:66 , VAL A:67 , SER A:68 , SUC A:9005 , HOH A:9012 , HOH A:9014 , HOH A:9029 , HOH A:9061
BINDING SITE FOR RESIDUE SUC A 9001
2
AC2
SOFTWARE
ARG A:38 , GLN A:43 , GLY A:44 , LEU A:45 , GLU A:46 , ARG A:62 , HOH A:9009 , HOH A:9010 , HOH A:9035 , HOH A:9145 , HOH A:9167 , THR B:97 , PHE B:98 , GLN B:100 , HOH B:278
BINDING SITE FOR RESIDUE SUC A 9002
3
AC3
SOFTWARE
ARG C:38 , GLN C:43 , GLY C:44 , LEU C:45 , GLU C:46 , HOH C:9009 , THR D:97 , PHE D:98 , GLN D:100 , HOH D:9020 , HOH D:9033 , HOH D:9041
BINDING SITE FOR RESIDUE SUC D 9003
4
AC4
SOFTWARE
TYR C:59 , GLN C:64 , GLY C:65 , ARG C:66 , VAL C:67 , SER C:68 , SUC C:9006 , HOH C:9016 , HOH C:9093
BINDING SITE FOR RESIDUE SUC C 9004
5
AC5
SOFTWARE
ASN A:55 , SER A:68 , ILE A:69 , THR A:70 , SUC A:9001 , HOH A:9012 , HOH A:9014 , HOH A:9033 , HOH A:9103 , HOH A:9134
BINDING SITE FOR RESIDUE SUC A 9005
6
AC6
SOFTWARE
ASN C:55 , TYR C:59 , SER C:68 , ILE C:69 , SUC C:9004 , HOH C:9016
BINDING SITE FOR RESIDUE SUC C 9006
7
AC7
SOFTWARE
GLY A:100H , MET A:100I , SER A:100J , TRP A:100K , HOH A:9066 , TRP B:32 , LYS B:50 , HIS B:91 , ASP B:92 , HOH B:389
BINDING SITE FOR RESIDUE SUC A 9007
8
AC8
SOFTWARE
CYS D:214 , ASP D:9005 , HOH D:9161
BINDING SITE FOR RESIDUE CYS D 9004
9
AC9
SOFTWARE
CYS D:9004 , HOH D:9122 , HOH D:9130 , HOH D:9161
BINDING SITE FOR RESIDUE ASP D 9005
[
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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1rzga2 (A:114-214)
1b: SCOP_d1rzgc2 (C:114-213)
2a: SCOP_d1rzgb2 (B:108-213)
2b: SCOP_d1rzgd2 (D:108-214)
3a: SCOP_d1rzga1 (A:1-113)
3b: SCOP_d1rzgc1 (C:2-113)
4a: SCOP_d1rzgb1 (B:1-107)
4b: SCOP_d1rzgd1 (D:1-107)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Human (Homo sapiens) [TaxId: 9606]
(179)
1a
d1rzga2
A:114-214
1b
d1rzgc2
C:114-213
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1rzgb2
B:108-213
2b
d1rzgd2
D:108-214
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Human (Homo sapiens), cluster 1 [TaxId: 9606]
(37)
3a
d1rzga1
A:1-113
3b
d1rzgc1
C:2-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Human (Homo sapiens), cluster 1 [TaxId: 9606]
(19)
4a
d1rzgb1
B:1-107
4b
d1rzgd1
D:1-107
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1rzgB02 (B:110-211)
1b: CATH_1rzgA02 (A:110-214)
1c: CATH_1rzgC02 (C:110-213)
1d: CATH_1rzgC01 (C:2-109)
1e: CATH_1rzgA01 (A:1-109)
1f: CATH_1rzgD02 (D:110-211)
1g: CATH_1rzgB01 (B:1-108)
1h: CATH_1rzgD01 (D:1-108)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
1rzgB02
B:110-211
1b
1rzgA02
A:110-214
1c
1rzgC02
C:110-213
1d
1rzgC01
C:2-109
1e
1rzgA01
A:1-109
1f
1rzgD02
D:110-211
1g
1rzgB01
B:1-108
1h
1rzgD01
D:1-108
[
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 (157 KB)
Header - Asym.Unit
Biol.Unit 1 (79 KB)
Header - Biol.Unit 1
Biol.Unit 2 (76 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
1RZG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
