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...
Getting 'PROSITE' information from database.
1GZL
Biol. Unit 2
Info
Asym.Unit (29 KB)
Biol.Unit 1 (34 KB)
Biol.Unit 2 (35 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 C14LINKMID/IQN17: A CROSS-LINKED INHIBITOR OF HIV-1 ENTRY BOUND TO THE GP41 HYDROPHOBIC POCKET
Authors
:
S. K. Sia, P. A. Carr, A. G. Cochran, V. M. Malashkevich, P. S. Kim
Date
:
23 May 02 (Deposition) - 10 Oct 02 (Release) - 02 Dec 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (3x)
Biol. Unit 2: B,D (3x)
Keywords
:
Glycoprotein, Hiv Entry, Inhibitor, Cross-Link, Gp41, Coiled Coil
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. K. Sia, P. A. Carr, A. G. Cochran, V. M. Malashkevich, P. S. Kim
Short Constrained Peptides That Inhibit Hiv-1 Entry
Proc. Natl. Acad. Sci. Usa V. 99 14664 2002
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
3a: PENTANE-1,5-DIAMINE (N2Pa)
3b: PENTANE-1,5-DIAMINE (N2Pb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
3
Mod. Amino Acid
ACETYL GROUP
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
N2P
3
Ligand/Ion
PENTANE-1,5-DIAMINE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ILE B:19
BINDING SITE FOR RESIDUE CL B1046
2
AC4
SOFTWARE
GLU D:629 , ASP D:632 , ARG D:633 , GLU D:636
BINDING SITE FOR RESIDUE N2P D1640
[
close Site info
]
SAPs(SNPs)/Variants
(1, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_GCN4_YEAST_004 (D7A, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_GCN4_YEAST_004
*
D
91
A
GCN4_YEAST
---
---
B
D
7
A
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: BZIP (B:38-40)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BZIP
PS50217
Basic-leucine zipper (bZIP) domain profile.
GCN4_YEAST
231-276
3
-
B:38-40
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d1gzl_1 (A:,C:)
1b: SCOP_d1gzl_2 (B:,D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Coiled coil proteins
(689)
Fold
:
Stalk segment of viral fusion proteins
(231)
Superfamily
:
Virus ectodomain
(48)
Family
:
Virus ectodomain
(44)
Protein domain
:
Retrovius gp41 protease-resistant core
(35)
Human immunodeficiency virus type 1 [TaxId: 11676]
(23)
1a
d1gzl.1
A:,C:
1b
d1gzl.2
B:,D:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1gzlA00 (A:1-45)
1b: CATH_1gzlB00 (B:1-45)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.170, no name defined]
(60)
[unclassified]
(20)
1a
1gzlA00
A:1-45
1b
1gzlB00
B:1-45
[
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 B
Chain D
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
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 (29 KB)
Header - Asym.Unit
Biol.Unit 1 (34 KB)
Header - Biol.Unit 1
Biol.Unit 2 (35 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
1GZL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help