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.
5MER
Biol. Unit 2
Info
Asym.Unit (290 KB)
Biol.Unit 1 (143 KB)
Biol.Unit 2 (143 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN LEUKOCYTE ANTIGEN A02 PRESENTING ILAKFLHEL
Authors
:
P. J. Rizkallah, A. Lloyd, M. Crowther, D. K. Cole, A. K. Sewell
Date
:
16 Nov 16 (Deposition) - 07 Dec 16 (Release) - 01 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.88
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Immune System, Hla, Tcr, Cross-Reactivity, Telomerase, Hla A02
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. K. Cole, H. A. Van Den Berg, A. Lloyd, M. D. Crowther, K. Beck, J. Ekeruche-Makinde, J. J. Miles, A. M. Bulek, G. Dolton, A. J. Schauenburg, A. Wall, A. Fuller, M. Clement, B. Laugel, P. J. Rizkallah, L. Wooldridge, A. K. Sewell
Structural Mechanism Underpinning Cross-Reactivity Of A Cd8 T-Cell Clone That Recognizes A Peptide Derived From Human Telomerase Reverse Transcriptase.
J. Biol. Chem. V. 292 802 2017
[
close entry info
]
Hetero Components
(4, 21)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
4a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
4b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
4c: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESc)
4d: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESd)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
EDO
10
Ligand/Ion
1,2-ETHANEDIOL
3
GOL
2
Ligand/Ion
GLYCEROL
4
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AD8 (SOFTWARE)
04: AD9 (SOFTWARE)
05: AE1 (SOFTWARE)
06: AE2 (SOFTWARE)
07: AE3 (SOFTWARE)
08: AE4 (SOFTWARE)
09: AE5 (SOFTWARE)
10: AE6 (SOFTWARE)
11: AE7 (SOFTWARE)
12: AE8 (SOFTWARE)
13: AE9 (SOFTWARE)
14: AF1 (SOFTWARE)
15: AF2 (SOFTWARE)
16: AF3 (SOFTWARE)
17: AF4 (SOFTWARE)
18: AF5 (SOFTWARE)
19: AF6 (SOFTWARE)
20: AF7 (SOFTWARE)
21: AF8 (SOFTWARE)
22: AF9 (SOFTWARE)
23: AG1 (SOFTWARE)
24: AG2 (SOFTWARE)
25: AG3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
MET A:138 , GLN A:141 , THR A:142 , HIS A:145 , HOH A:514 , ARG E:45 , ARG E:81 , HOH E:210
binding site for residue MES A 304
02
AC6
SOFTWARE
ASP B:96 , HOH B:203 , GLU E:74 , LYS E:75
binding site for residue EDO B 102
03
AD8
SOFTWARE
TRP A:167 , LYS C:4 , HOH C:201 , ARG D:131 , ARG D:157
binding site for residue SO4 C 103
04
AD9
SOFTWARE
VAL D:231 , GLU D:232 , HOH D:418 , HOH D:481 , HOH D:503 , HOH D:514 , GLN E:8
binding site for residue GOL D 301
05
AE1
SOFTWARE
ASP D:122 , TYR D:123 , ILE D:124 , ALA D:125 , THR D:134 , ALA D:136 , HOH D:404 , HOH D:457
binding site for residue EDO D 302
06
AE2
SOFTWARE
HIS D:188 , THR D:190 , TRP D:204 , ASP E:98 , EDO E:102
binding site for residue EDO D 303
07
AE3
SOFTWARE
ARG A:157 , THR D:163 , TRP D:167 , HOH D:403 , LYS F:4
binding site for residue EDO D 304
08
AE4
SOFTWARE
TYR D:85 , TYR D:118 , LYS D:121 , ASP D:122 , TYR D:123 , ASP D:137
binding site for residue EDO D 305
09
AE5
SOFTWARE
ARG D:14 , GLY D:16 , GLY D:18 , HOH D:465 , HOH D:549 , HOH D:550
binding site for residue CA D 306
10
AE6
SOFTWARE
GLY B:43 , GLU B:44 , ARG B:45 , ARG B:81 , THR D:142 , HIS D:145 , HOH D:546
binding site for residue MES D 307
11
AE7
SOFTWARE
ARG A:35 , ALA A:40 , ALA A:41 , SER D:88 , HOH D:415 , HOH D:419
binding site for residue SO4 D 308
12
AE8
SOFTWARE
GLU D:232 , THR D:233 , LYS D:243 , MES E:107 , SO4 E:108
binding site for residue SO4 D 309
13
AE9
SOFTWARE
ASN B:17 , GLU B:74 , HIS D:191 , HIS D:192 , ALA D:193 , HOH D:435 , HOH D:459
binding site for residue SO4 D 310
14
AF1
SOFTWARE
SER A:88 , ARG D:35 , ALA D:40 , ALA D:41 , HOH D:420 , HOH D:445 , HOH D:483
binding site for residue SO4 D 311
15
AF2
SOFTWARE
SER D:2 , HIS D:3 , ARG D:6 , ASP D:102 , HOH D:430 , HOH D:450
binding site for residue SO4 D 312
16
AF3
SOFTWARE
ARG D:6 , PHE D:8 , TYR D:27 , ASP D:29 , ASP D:30 , HOH D:437 , MES E:107
binding site for residue SO4 D 313
17
AF4
SOFTWARE
HIS A:191 , HIS A:192 , ALA A:193 , ASN E:17 , HOH E:221
binding site for residue GOL E 101
18
AF5
SOFTWARE
TRP D:204 , LEU D:206 , ARG D:234 , GLN D:242 , EDO D:303 , TYR E:10 , SER E:11 , HIS E:13 , PRO E:14 , HOH E:232 , HOH E:240
binding site for residue EDO E 102
19
AF6
SOFTWARE
GLU E:74 , TRP E:95 , ASP E:96 , ARG E:97
binding site for residue EDO E 103
20
AF7
SOFTWARE
GLN E:8 , VAL E:9 , LYS E:94 , ASP E:96 , HOH E:220
binding site for residue EDO E 104
21
AF8
SOFTWARE
LEU E:40 , ASN E:42 , GLY E:43 , GLU E:77
binding site for residue EDO E 105
22
AF9
SOFTWARE
GLN D:115 , SER E:57 , LYS E:58
binding site for residue EDO E 106
23
AG1
SOFTWARE
THR D:233 , SO4 D:309 , SO4 D:313 , TYR E:26 , SER E:57 , LYS E:58 , SO4 E:108 , HOH E:226
binding site for residue MES E 107
24
AG2
SOFTWARE
SO4 D:309 , HOH D:467 , SER E:57 , LYS E:58 , ASP E:59 , MES E:107 , HOH E:215
binding site for residue SO4 E 108
25
AG3
SOFTWARE
ARG D:97 , TRP D:147 , VAL D:152 , LEU F:6 , HIS F:7 , HOH F:206
binding site for residue EDO F 101
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
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 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 (290 KB)
Header - Asym.Unit
Biol.Unit 1 (143 KB)
Header - Biol.Unit 1
Biol.Unit 2 (143 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
5MER
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help