6APN
Single chain construct of HLA-A*02:01 binding "None" at 2.22Å resolution
Data provenance
Structure downloaded from PDB Europe using the Coordinate Server.
Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4.
Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6.
Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint.
Structure visualised with 3DMol7.
Information sections
Complex type
Single chain class i construct
1. Class I alpha
HLA-A*02:01
HLA-A*02:01
['A', 'B']
Species
Locus / Allele group
Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
|
A Pocket
GLY159
PRO163
ALA167
VAL171
THR5
ILE59
LEU63
ASN66
GLY7
|
B Pocket
SER24
TYR34
ASN45
LEU63
ASN66
GLY67
GLY7
ILE70
VAL9
LYS99
|
C Pocket
ILE70
VAL73
GLU74
VAL9
THR97
|
D Pocket
PRO114
VAL155
SER156
GLY159
ARG160
LYS99
|
E Pocket
PRO114
SER147
PHE152
SER156
THR97
|
F Pocket
ILE116
MET123
SER143
HIS146
SER147
ASP77
PHE80
SER81
TRP84
THR95
|
Colour key
Binds N-terminus
Binds P1 backbone
Binds P2 backbone
Binds PC-1 backbone
Binds C-terminus
Data provenance
N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.
|
1. Class I alpha
HLA-A*02:01
IPD-IMGT/HLA
[ipd-imgt:HLA35266] |
10 20 30 40 50 60
LLMGTLGIVGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIE 70 80 90 100 110 120 VDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWD 130 140 150 160 170 180 RDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFD 190 200 210 220 230 240 SDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGAYNQSEAGSHTVQR 250 260 270 280 290 300 MYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLR 310 320 330 340 350 360 AYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTW 370 380 390 400 410 420 QRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEEN 430 440 LYFQGHHHHHHGLNDIFEAQKIEWHE |
Data provenance
Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.
Downloadable data
Data can be downloaded to your local machine from the links below.
Clicking on the clipboard icon will copy the url for the data to your clipboard.
This can then be used to load the structure/data directly from the url into an application like PyMol (for 3D structures) using the load command:
e.g. load http://www.histo.fyi/structures/downloads/1hhk_1_peptide.cif
or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.
Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.
Components
MHC Class I alpha chain [cif]
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
Data license
The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.
Footnotes
- Protein Data Bank Europe - Coordinate Server
- 1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
- Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
- PyMol - PyMol.org/pymol
- Levenshtein distance - Wikipedia entry
- Protein Data Bank Europe REST API - Molecules endpoint
- 3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
- Protein Data Bank Europe REST API - Publication endpoint
- PubMed Central Europe REST API - Articles endpoint
This work is licensed under a Creative Commons Attribution 4.0 International License.