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3P4M

H2-Kb binding "YTVKYPNL" at 2.50Å 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.

Information sections

Complex type

Class i with peptide

1. Beta 2 microglobulin
['B', 'E']
2. Class I alpha
H2-Kb
['A', 'D']
3. Peptide
YTVKYPNL
['C', 'F']

Species

Locus / Allele group

H2-K / H2-Kb

Publication

Crystal Structure of H2-Kb in complex with the NP205-LCMV epitope YTVKYPNL, an 8-mer peptide from the LCMV

Gras, S., Guillonneau, C., Rossjohn, J.

Structure deposition and release

Deposited: 2010-10-06
Released: 2011-10-12
Revised: 2011-10-12

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Octamer (8 amino acids)

Sequence: YTVKYPNL

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 TYR

TYR159
TYR7
THR163
LYS66
GLU63
TRP167
LEU5
TYR171
ARG62
TYR59
 P2 THR

GLU24
TYR45
TYR159
TYR7
ASN70
LYS66
GLU63
 P3 VAL

GLN114
ASN70
ARG155
TYR159
SER99
LEU156
LYS66
 P4 LYS

ASN70
LYS66
ARG155
 P5 TYR

VAL9
GLN114
GLU24
ARG155
TYR22
VAL97
SER73
SER99
PHE74
TYR116
TYR7
ASN70
 P6 PRO

SER73
TRP147
TYR116
GLU152
ASP77
GLN114
ARG155
 P7 ASN

SER73
THR143
ASP77
TRP147
VAL76
LYS146
 P8 LEU

THR143
TRP147
THR80
TYR116
LEU81
ASP77
TYR84
TYR123
LYS146
ILE95

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

MET24
PHE34
ARG45
ARG63
GLN66
LYS67
ARG7
GLY70
PHE9
ILE99
C Pocket

GLY70
GLN73
SER74
PHE9
GLN97
D Pocket

TYR114
GLU155
ARG156
ALA159
TYR160
ILE99
E Pocket

TYR114
LYS147
GLY152
ARG156
GLN97
F Pocket

GLN116
ASP123
ILE143
HIS146
LYS147
VAL77
ARG80
THR81
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
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDW
        70        80        90
SFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM
2. Class I alpha
H2-Kb
        10        20        30        40        50        60
MGPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEY
        70        80        90       100       110       120
WERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYD
       130       140       150       160       170       180
GCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATL
       190       200       210       220       230       240
LRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDG
       250       260       270
TFQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRWEPP
3. Peptide
YTVKYPNL

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]
  1. 3P4M assembly 1  
  2. 3P4M assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 3P4M assembly 1  
  2. 3P4M assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 3P4M assembly 1  
  2. 3P4M assembly 2  
Peptide only [cif]
  1. 3P4M assembly 1  
  2. 3P4M assembly 2  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/3p4m

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


Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.