6MPP

HLA-A*01:01 binding "ILDTAGKEEY"

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

Class i with peptide

1. Beta 2 microglobulin

['C']

2. Class I alpha
HLA-A*01:01

['A']

3. Peptide
ILDTAGKEEY

['B']

Species

Homo sapiens (Human)

Locus / Allele group

HLA-A / HLA-A*01

Publication

MHC-I complex determined by NMR

Flores-Solis, D., McShan, A.C., Sgourakis, N.G.

Structure deposition and release

Deposited: 2018-10-08

Released: 2019-10-16

Revised: 2022-03-16

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Decamer (10 amino acids)

Sequence: ILDTAGKEEY

Interactive view

Cutaway side view (static)

Surface top view (static - coloured by atom property)

Cutaway top view (static)

Data provenance

MHC:peptide complexes are visualised using PyMol. The peptide is superimposed on a consistent cutaway slice of the MHC binding cleft (displayed as a grey mesh) which best indicates the binding pockets for the P1/P5/PC positions (side view - pockets A, E, F) and for the P2/P3/PC-2 positions (top view - pockets B, C, D). In some cases peptides will use a different pocket for a specific peptide position (atypical anchoring). On some structures the peptide may appear to sterically clash with a pocket. This is an artefact of picking a standardised slice of the cleft and overlaying the peptide.

Peptide neighbours

P1 ILE

ASP166

PHE33

TYR171

VAL34

TYR59

TYR7

CYS164

TYR99

ARG163

MET45

GLY167

MET5

GLU55

ARG170

GLU63

TYR159

ILE52

P10 TYR

ARG114

TYR84

THR143

ILE95

THR80

LYS146

ILE124

ILE97

TYR123

ASP116

TRP147

LEU81

ILE142

ALA117

ASN77

ALA139

TYR118

P2 LEU

ARG163

ALA24

MET45

TYR99

ASN66

THR64

GLU63

MET67

VAL34

HIS70

TYR159

PHE9

PHE36

TYR7

GLY26

PHE33

P3 ASP

TYR159

PHE9

TYR99

ARG163

LEU160

GLN155

ASN66

HIS70

ARG156

P4 THR

ALA69

GLN155

ASN66

HIS70

ARG156

TYR159

GLN62

ARG163

P5 ALA

ALA69

THR73

ASN66

HIS70

ARG156

P6 GLY

GLN155

HIS70

ARG156

THR73

P7 LYS

ALA152

GLN155

ARG156

TRP147

VAL150

P8 GLU

ARG114

ARG156

HIS70

ILE97

TRP147

THR73

ASN77

P9 GLU

ASN77

THR143

ALA76

TRP147

LYS146

THR73

Colour key

Aromatic Hydrophobic Acidic Basic Neutral/polar

Data provenance

Neighbours are calculated by finding residues with atoms within 5Å of each other using BioPython Neighboursearch module. The list of neighbours is then sorted and filtered to inlcude only neighbours where between the peptide and the MHC Class I alpha chain.

Colours selected to match the YRB scheme. [https://www.frontiersin.org/articles/10.3389/fmolb.2015.00056/full]

Binding cleft pockets

Peptide sidechain binding pockets (static)

Peptide terminii and backbone binding residues (static)

A Pocket

TYR159

ARG163

GLY167

TYR171

MET5

TYR59

GLU63

ASN66

TYR7

B Pocket

ALA24

VAL34

MET45

GLU63

ASN66

MET67

TYR7

HIS70

PHE9

TYR99

C Pocket

HIS70

THR73

ASP74

PHE9

ILE97

D Pocket

ARG114

GLN155

ARG156

TYR159

LEU160

TYR99

E Pocket

ARG114

TRP147

ALA152

ARG156

ILE97

F Pocket

ASP116

TYR123

THR143

LYS146

TRP147

ASN77

THR80

LEU81

TYR84

ILE95

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. Beta 2 microglobulin Beta 2 microglobulin	10 20 30 40 50 60 MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

2. Class I alpha HLA-A01:01 IPD-IMGT/HLA* [ipd-imgt:HLA34767]	10 20 30 40 50 60 GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYW 70 80 90 100 110 120 DQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG 130 140 150 160 170 180 KDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQ 190 200 210 220 230 240 RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT 250 260 270 FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSSQ

3. Peptide	ILDTAGKEEY

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.

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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.

Complete structures

Aligned structures [cif]

6MPP assembly 1

Components

MHC Class I alpha chain [cif]

6MPP assembly 1

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

6MPP assembly 1

Peptide only [cif]

6MPP assembly 1

Derived data

Data for this page [json]

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

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.