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.
3NTE
Asym. Unit
Info
Asym.Unit (154 KB)
Biol.Unit 1 (149 KB)
Biol.Unit 2 (148 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 THE WILD-TYPE FULL-LENGTH HIV-1 CAPSID PROTEIN
Authors
:
L. Betts, J. I. Yeh
Date
:
03 Jul 10 (Deposition) - 01 Dec 10 (Release) - 02 Jul 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (1x)
Keywords
:
Wild Type Viral Protein, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Du, L. Betts, R. Yang, H. Shi, J. Concel, J. Ahn, C. Aiken, P. Zhang, J. I. Yeh
Structure Of The Hiv-1 Full-Length Capsid Protein In A Conformationally Trapped Unassembled State Induced By Small-Molecule Binding.
J. Mol. Biol. V. 406 371 2011
[
close entry info
]
Hetero Components
(4, 43)
Info
All Hetero Components
1a: FE (III) ION (FEa)
1b: FE (III) ION (FEb)
1c: FE (III) ION (FEc)
1d: FE (III) ION (FEd)
1e: FE (III) ION (FEe)
1f: FE (III) ION (FEf)
1g: FE (III) ION (FEg)
1h: FE (III) ION (FEh)
1i: FE (III) ION (FEi)
1j: FE (III) ION (FEj)
1k: FE (III) ION (FEk)
1l: FE (III) ION (FEl)
1m: FE (III) ION (FEm)
1n: FE (III) ION (FEn)
1o: FE (III) ION (FEo)
1p: FE (III) ION (FEp)
1q: FE (III) ION (FEq)
1r: FE (III) ION (FEr)
1s: FE (III) ION (FEs)
1t: FE (III) ION (FEt)
1u: FE (III) ION (FEu)
1v: FE (III) ION (FEv)
1w: FE (III) ION (FEw)
2a: TRI-IODODE ANION (I3Ma)
2b: TRI-IODODE ANION (I3Mb)
3a: IODIDE ION (IODa)
3b: IODIDE ION (IODb)
3c: IODIDE ION (IODc)
3d: IODIDE ION (IODd)
3e: IODIDE ION (IODe)
3f: IODIDE ION (IODf)
3g: IODIDE ION (IODg)
3h: IODIDE ION (IODh)
3i: IODIDE ION (IODi)
3j: IODIDE ION (IODj)
3k: IODIDE ION (IODk)
3l: IODIDE ION (IODl)
3m: IODIDE ION (IODm)
3n: IODIDE ION (IODn)
3o: IODIDE ION (IODo)
3p: IODIDE ION (IODp)
3q: IODIDE ION (IODq)
4a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
23
Ligand/Ion
FE (III) ION
2
I3M
2
Ligand/Ion
TRI-IODODE ANION
3
IOD
17
Ligand/Ion
IODIDE ION
4
NA
1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(40, 40)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:178
BINDING SITE FOR RESIDUE IOD A 222
02
AC2
SOFTWARE
IOD A:230 , FE A:243 , HOH A:260
BINDING SITE FOR RESIDUE IOD A 223
03
AC3
SOFTWARE
HOH A:302 , HOH B:281
BINDING SITE FOR RESIDUE IOD A 224
04
AC4
SOFTWARE
PRO A:1 , HOH A:341
BINDING SITE FOR RESIDUE IOD A 225
05
AC5
SOFTWARE
ARG A:173 , LYS A:182
BINDING SITE FOR RESIDUE IOD A 226
06
AC6
SOFTWARE
LYS A:158 , FE A:239
BINDING SITE FOR RESIDUE IOD A 227
07
AC7
SOFTWARE
FE A:241
BINDING SITE FOR RESIDUE IOD A 228
08
AC8
SOFTWARE
ASN A:74 , HOH A:332 , HOH A:333
BINDING SITE FOR RESIDUE IOD A 229
09
AC9
SOFTWARE
ILE A:129 , IOD A:223
BINDING SITE FOR RESIDUE IOD A 230
10
BC1
SOFTWARE
ILE A:37 , HOH A:321 , HOH A:336
BINDING SITE FOR RESIDUE IOD A 231
11
BC2
SOFTWARE
FE A:245 , FE A:247
BINDING SITE FOR RESIDUE IOD A 232
12
BC3
SOFTWARE
FE A:247 , HOH A:260
BINDING SITE FOR RESIDUE IOD A 233
13
BC4
SOFTWARE
VAL A:142 , HOH A:265 , HOH A:325
BINDING SITE FOR RESIDUE I3M A 234
14
BC5
SOFTWARE
HOH A:323
BINDING SITE FOR RESIDUE FE A 235
15
BC6
SOFTWARE
MET A:118 , PRO A:125 , GLY A:127 , GLU A:128 , HOH A:312
BINDING SITE FOR RESIDUE FE A 237
16
BC7
SOFTWARE
GLU A:35 , PRO B:34 , VAL B:142 , HOH B:262 , HOH B:281
BINDING SITE FOR RESIDUE FE A 238
17
BC8
SOFTWARE
IOD A:227
BINDING SITE FOR RESIDUE FE A 239
18
BC9
SOFTWARE
ASN A:53 , ASN A:57
BINDING SITE FOR RESIDUE FE A 240
19
CC1
SOFTWARE
IOD A:228 , HOH A:331
BINDING SITE FOR RESIDUE FE A 241
20
CC2
SOFTWARE
HOH A:278 , HOH B:261
BINDING SITE FOR RESIDUE FE A 242
21
CC3
SOFTWARE
IOD A:223 , HOH A:260
BINDING SITE FOR RESIDUE FE A 243
22
CC4
SOFTWARE
ILE A:15 , SER A:16 , THR A:19 , HOH A:341 , HOH A:342
BINDING SITE FOR RESIDUE FE A 244
23
CC5
SOFTWARE
IOD A:232
BINDING SITE FOR RESIDUE FE A 245
24
CC6
SOFTWARE
HIS A:87 , HOH A:376
BINDING SITE FOR RESIDUE FE A 246
25
CC7
SOFTWARE
IOD A:232 , IOD A:233
BINDING SITE FOR RESIDUE FE A 247
26
CC8
SOFTWARE
ILE B:6
BINDING SITE FOR RESIDUE IOD B 222
27
CC9
SOFTWARE
SER B:178
BINDING SITE FOR RESIDUE IOD B 223
28
DC1
SOFTWARE
PRO B:157 , LYS B:158 , GLU B:159 , HOH B:265
BINDING SITE FOR RESIDUE IOD B 224
29
DC2
SOFTWARE
HIS B:62
BINDING SITE FOR RESIDUE IOD B 226
30
DC3
SOFTWARE
PHE B:32 , HOH B:295
BINDING SITE FOR RESIDUE I3M B 227
31
DC4
SOFTWARE
ASN B:74 , HOH B:305
BINDING SITE FOR RESIDUE FE B 228
32
DC5
SOFTWARE
MET B:118 , PRO B:125 , GLY B:127 , GLU B:128 , HOH B:258
BINDING SITE FOR RESIDUE FE B 229
33
DC6
SOFTWARE
ARG B:162
BINDING SITE FOR RESIDUE FE B 230
34
DC7
SOFTWARE
HOH B:260
BINDING SITE FOR RESIDUE FE B 231
35
DC8
SOFTWARE
HOH A:250 , ARG B:173
BINDING SITE FOR RESIDUE FE B 233
36
DC9
SOFTWARE
ARG B:132 , HOH B:285
BINDING SITE FOR RESIDUE FE B 234
37
EC1
SOFTWARE
GLY B:46 , GLU B:128 , LYS B:131
BINDING SITE FOR RESIDUE FE B 235
38
EC2
SOFTWARE
ASP A:163 , HOH A:288 , GLY B:220 , HOH B:290
BINDING SITE FOR RESIDUE FE B 236
39
EC3
SOFTWARE
ILE B:124 , HOH B:247
BINDING SITE FOR RESIDUE FE B 237
40
EC4
SOFTWARE
ASN B:74
BINDING SITE FOR RESIDUE NA B 238
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3ntea2 (A:148-221)
1b: SCOP_d3nteb2 (B:148-221)
2a: SCOP_d3ntea1 (A:1-147)
2b: SCOP_d3nteb1 (B:1-147)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Acyl carrier protein-like
(148)
Superfamily
:
Retrovirus capsid dimerization domain-like
(45)
Family
:
automated matches
(12)
Protein domain
:
automated matches
(12)
Human immunodeficiency virus 1 [TaxId: 11676]
(3)
1a
d3ntea2
A:148-221
1b
d3nteb2
B:148-221
Fold
:
Retrovirus capsid protein, N-terminal core domain
(53)
Superfamily
:
Retrovirus capsid protein, N-terminal core domain
(53)
Family
:
Retrovirus capsid protein, N-terminal core domain
(51)
Protein domain
:
automated matches
(14)
Human immunodeficiency virus 1 [TaxId: 11676]
(7)
2a
d3ntea1
A:1-147
2b
d3nteb1
B:1-147
[
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
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 (154 KB)
Header - Asym.Unit
Biol.Unit 1 (149 KB)
Header - Biol.Unit 1
Biol.Unit 2 (148 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
3NTE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
