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.
PLEASE WAIT...
Getting 'Exon' information from database.
1QVO
Asym. Unit
Info
Asym.Unit (141 KB)
Biol.Unit 1 (271 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURES OF HLA-A*1101 IN COMPLEX WITH IMMUNODOMINANT NONAMER AND DECAMER HIV-1 EPITOPES CLEARLY REVEAL THE PRESENCE OF A MIDDLE ANCHOR RESIDUE
Authors
:
L. Li, J. M. Mcnicholl, M. Bouvier
Date
:
28 Aug 03 (Deposition) - 01 Jun 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.22
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (2x)
Keywords
:
Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Li, M. Bouvier
Structures Of Hla-A*1101 Complexed With Immunodominant Nonamer And Decamer Hiv-1 Epitopes Clearly Reveal The Presence Of A Middle, Secondary Anchor Residue.
J. Immunol. V. 172 6175 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(14, 28)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004353 (E19K, chain A/D, )
02: VAR_056254 (R65G, chain A/D, )
03: VAR_056255 (Q70H, chain A/D, )
04: VAR_056256 (D77N, chain A/D, )
05: VAR_056257 (G107W, chain A/D, )
06: VAR_016731 (F109L, chain A/D, )
07: VAR_056258 (N127K, chain A/D, )
08: VAR_056259 (I142T, chain A/D, )
09: VAR_016732 (K144E, chain A/D, )
10: VAR_056260 (R145H, chain A/D, )
11: VAR_016733 (H151R, chain A/D, )
12: VAR_016734 (A152E, chain A/D, )
13: VAR_016735 (R163T, chain A/D, )
14: VAR_056261 (R181H, chain A/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_004353
E
43
K
1A11_HUMAN
Polymorphism
---
A/D
E
19
K
02
UniProt
VAR_056254
R
89
G
1A11_HUMAN
Polymorphism
1059459
A/D
R
65
G
03
UniProt
VAR_056255
Q
94
H
1A11_HUMAN
Polymorphism
1059463
A/D
Q
70
H
04
UniProt
VAR_056256
D
101
N
1A11_HUMAN
Polymorphism
1136688
A/D
D
77
N
05
UniProt
VAR_056257
G
131
W
1A11_HUMAN
Polymorphism
1136702
A/D
G
107
W
06
UniProt
VAR_016731
F
133
L
1A11_HUMAN
Polymorphism
1059488
A/D
F
109
L
07
UniProt
VAR_056258
N
151
K
1A11_HUMAN
Polymorphism
1059509
A/D
N
127
K
08
UniProt
VAR_056259
I
166
T
1A11_HUMAN
Polymorphism
1059516
A/D
I
142
T
09
UniProt
VAR_016732
K
168
E
1A11_HUMAN
Polymorphism
---
A/D
K
144
E
10
UniProt
VAR_056260
R
169
H
1A11_HUMAN
Polymorphism
1059520
A/D
R
145
H
11
UniProt
VAR_016733
H
175
R
1A11_HUMAN
Polymorphism
---
A/D
H
151
R
12
UniProt
VAR_016734
A
176
E
1A11_HUMAN
Polymorphism
---
A/D
A
152
E
13
UniProt
VAR_016735
R
187
T
1A11_HUMAN
Polymorphism
---
A/D
R
163
T
14
UniProt
VAR_056261
R
205
H
1A11_HUMAN
Polymorphism
17185861
A/D
R
181
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84,E:78-84,A:257-263,D:257-26...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
B2MG_HUMAN
98-104
2
B:78-84
E:78-84
1A11_HUMAN
281-287
2
A:257-263
D:257-263
[
close PROSITE info
]
Exons
(5, 10)
Info
All Exons
Exon 1.3d (A:1-1 | D:1-1)
Exon 1.4b (A:1-91 | D:1-91)
Exon 1.4e (A:91-183 | D:91-183)
Exon 1.5 (A:183-275 | D:183-275)
Exon 1.6a (A:275-275 | D:275-275)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.3d
2: Boundary 1.3d/1.4b
3: Boundary 1.4b/1.4e
4: Boundary 1.4e/1.5
5: Boundary 1.5/1.6a
6: Boundary 1.6a/1.6d
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.3d
ENST00000376809
3d
ENSE00001674356
chr6:
29910287-29910403
117
1A11_HUMAN
1-25
25
2
A:1-1
D:1-1
1
1
1.4b
ENST00000376809
4b
ENSE00001709288
chr6:
29910534-29910803
270
1A11_HUMAN
25-115
91
2
A:1-91
D:1-91
91
91
1.4e
ENST00000376809
4e
ENSE00001681031
chr6:
29911045-29911320
276
1A11_HUMAN
115-207
93
2
A:91-183
D:91-183
93
93
1.5
ENST00000376809
5
ENSE00001789740
chr6:
29911899-29912174
276
1A11_HUMAN
207-299
93
2
A:183-275
D:183-275
93
93
1.6a
ENST00000376809
6a
ENSE00001725298
chr6:
29912277-29912393
117
1A11_HUMAN
299-338
40
2
A:275-275
D:275-275
1
1
1.6d
ENST00000376809
6d
ENSE00001649179
chr6:
29912836-29912868
33
1A11_HUMAN
338-349
12
0
-
-
1.7
ENST00000376809
7
ENSE00001689328
chr6:
29913011-29913058
48
1A11_HUMAN
349-365
17
0
-
-
1.8a
ENST00000376809
8a
ENSE00001755635
chr6:
29913228-29913617
390
1A11_HUMAN
365-365
1
0
-
-
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1qvob_ (B:)
1b: SCOP_d1qvoe_ (E:)
2a: SCOP_d1qvoa1 (A:182-275)
2b: SCOP_d1qvod1 (D:182-275)
3a: SCOP_d1qvoa2 (A:1-181)
3b: SCOP_d1qvod2 (D:1-181)
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
:
beta2-microglobulin
(530)
Human (Homo sapiens) [TaxId: 9606]
(350)
1a
d1qvob_
B:
1b
d1qvoe_
E:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Human (Homo sapiens) [TaxId: 9606]
(187)
2a
d1qvoa1
A:182-275
2b
d1qvod1
D:182-275
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
Class I MHC, alpha-1 and alpha-2 domains
(294)
Human (Homo sapiens), HLA-A11 [TaxId: 9606]
(4)
3a
d1qvoa2
A:1-181
3b
d1qvod2
D:1-181
[
close SCOP info
]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1qvoA01 (A:1-181)
1b: CATH_1qvoD01 (D:1-181)
2a: CATH_1qvoB00 (B:0-99)
2b: CATH_1qvoE00 (E:0-99)
2c: CATH_1qvoA02 (A:182-275)
2d: CATH_1qvoD02 (D:182-275)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
(402)
Homologous Superfamily
:
Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1
(400)
Human (Homo sapiens)
(249)
1a
1qvoA01
A:1-181
1b
1qvoD01
D:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1qvoB00
B:0-99
2b
1qvoE00
E:0-99
2c
1qvoA02
A:182-275
2d
1qvoD02
D:182-275
[
close CATH info
]
Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_C1_set_1qvoD01 (D:185-271)
1b: PFAM_C1_set_1qvoD02 (D:185-271)
1c: PFAM_C1_set_1qvoE01 (E:11-92)
1d: PFAM_C1_set_1qvoE02 (E:11-92)
2a: PFAM_MHC_I_1qvoD03 (D:1-179)
2b: PFAM_MHC_I_1qvoD04 (D:1-179)
3a: PFAM_F_protein_1qvoF01 (F:1-10)
3b: PFAM_F_protein_1qvoF02 (F:1-10)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Homo sapiens (Human)
(218)
1a
C1-set-1qvoD01
D:185-271
1b
C1-set-1qvoD02
D:185-271
1c
C1-set-1qvoE01
E:11-92
1d
C1-set-1qvoE02
E:11-92
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
2a
MHC_I-1qvoD03
D:1-179
2b
MHC_I-1qvoD04
D:1-179
Clan
:
no clan defined [family: F-protein]
(7)
Family
:
F-protein
(7)
Human immunodeficiency virus type 1 group M subtype D (isolate Z6) (HIV-1)
(1)
3a
F-protein-1qvoF01
F:1-10
3b
F-protein-1qvoF02
F:1-10
[
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
Chain E
Chain F
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 (141 KB)
Header - Asym.Unit
Biol.Unit 1 (271 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
1QVO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
