6E1I

Single chain construct of HLA-A*02:01 with H2-K alpha 3 domain binding "None" at 1.99Å 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.

Complex type

Single chain class i construct

1. Class I alpha
HLA-A*02:01 with H2-K alpha 3 domain

['A']

Species

Mus musculus (Mouse)

Locus / Allele group

HLA-A / HLA-A*02

Publication

HLA-A*0201 single chain trimer with murine H2K alpha 3 domain and HPV.16 E7 peptide YMLDLQPET

Finton, K.A.K., Rusnac, D.V.

Structure deposition and release

Deposited: 2018-07-09

Released: 2019-07-17

Revised: 2019-07-17

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Binding cleft pockets

Peptide sidechain binding pockets (static)

Peptide terminii and backbone binding residues (static)

A Pocket

GLY159

SER163

SER167

PHE171

THR5

PRO59

LYS63

ILE66

LEU7

B Pocket

ASP24

SER34

ILE45

LYS63

ILE66

LEU67

LEU7

TYR70

TRP9

SER99

C Pocket

TYR70

GLN73

PHE74

TRP9

ASP97

D Pocket

PHE114

GLY155

GLY156

GLY159

GLY160

SER99

E Pocket

PHE114

GLY147

GLY152

GLY156

ASP97

F Pocket

PRO116

ALA123

MET143

GLY146

GLY147

SER77

GLU80

ILE81

LEU84

MET95

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.

Chain sequences

1. Class I alpha

HLA-A*02:01 with H2-K alpha 3 domain

        10        20        30        40        50        60
METDTLLLWVLLLWVPGSTGYMLDLQPETGGGGSGGGGSGGGGSIQRTPQIQVYSRHPPE
        70        80        90       100       110       120
NGKPNILNCYVTQFHPSDIEIQMLKNGKKIPKVEMSDLSFSKDWSFYILAHTEFTPTETD
       130       140       150       160       170       180
TYACRVKHASMAEPKTVYWDRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGR
       190       200       210       220       230       240
GEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVD
       250       260       270       280       290       300
LGTLRGAYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAAD
       310       320       330       340       350       360
MAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDSPKAHVTYHPRSQV
       370       380       390       400       410       420
DVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTFQKWAAVVVPLGKEQNY
       430       440
TCHVHHEGLPEPLTLRWENLYF

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

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Complete structures

Aligned structures [cif]

6E1I assembly 1

Components

MHC Class I alpha chain [cif]

6E1I assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

6E1I assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/6e1i

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.