5IEH

HLA-B*40:02 binding "REFSKEPEL" at 1.50Å 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

Class i with peptide

1. Beta 2 microglobulin

['B']

2. Class I alpha
HLA-B*40:02

['A']

3. Peptide
REFSKEPEL

['C']

Species

Homo sapiens (Human)

Locus / Allele group

HLA-B / HLA-B*40

Publication

Structure of HLA-B*40:02 in complex with the phosphorilated endogenous peptide REFpSKEPEL

Alpizar, A., Marcilla, M., Santiago, C.

Structure deposition and release

Deposited: 2016-02-25

Released: 2016-12-07

Revised: 2019-10-16

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Nonamer (9 amino acids)

Sequence: REFSKEPEL

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 ARG

GLU63

TRP167

PHE33

TYR159

ARG62

TYR171

TYR7

GLU163

CYS164

TYR99

TYR59

ILE66

MET5

P2 GLU

THR24

TYR99

ILE66

LYS45

GLU63

SER67

ARG62

HIS9

VAL34

TYR159

TYR7

GLU163

ASN70

P3 PHE

TYR159

TYR7

GLU163

ARG62

ILE66

VAL152

LEU156

ASN70

GLN155

TYR99

P5 LYS

VAL152

GLN155

P6 GLU

ASN114

ASN70

TYR99

TYR74

THR73

SER97

HIS9

TYR116

ILE66

P7 PRO

VAL152

LEU156

THR73

TYR116

SER77

TRP147

P8 GLU

THR143

THR73

GLU76

TRP147

ASN80

SER77

LYS146

P9 LEU

ILE142

TYR84

SER77

THR143

LEU95

TYR74

LYS146

TYR123

ASN80

LEU81

THR73

ILE124

TRP147

TYR116

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

ALA159

GLY163

GLU167

ARG171

SER5

GLU59

ARG63

GLN66

ARG7

B Pocket

ILE24

PHE34

ALA45

ARG63

GLN66

ILE67

ARG7

THR70

PHE9

MET99

C Pocket

THR70

GLN73

THR74

PHE9

GLN97

D Pocket

HIS114

GLU155

GLN156

ALA159

TYR160

MET99

E Pocket

HIS114

LYS147

ARG152

GLN156

GLN97

F Pocket

GLN116

ASP123

ILE143

ARG146

LYS147

GLU77

ARG80

ASN81

GLY84

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.

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-B40:02 IPD-IMGT/HLA* [ipd-imgt:HLA33957]	10 20 30 40 50 60 MGSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDATSPAKEPRAPWIEQEGPEY 70 80 90 100 110 120 WDRETQISKTNTQTYRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHNQYAYD 130 140 150 160 170 180 GKDYIALNEDLRSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETL 190 200 210 220 230 240 QRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDR 250 260 270 TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide	REFSKEPEL

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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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]

5IEH assembly 1

Components

MHC Class I alpha chain [cif]

5IEH assembly 1

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

5IEH assembly 1

Peptide only [cif]

5IEH assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/5ieh

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.