H2-Kb binding "SIINFEKL" with Ly49c NK receptor at 3.26Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Class i with peptide and ly49c
H2-Kb
SIINFEKL
Species
Locus / Allele group
Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2K(b).
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
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
SER
GLU63
LEU5
TRP167
TYR159
TYR59
TYR7
LYS66
TYR171
|
P2
ILE
ASN70
TYR159
TYR7
LYS66
VAL9
GLU24
TYR22
GLU63
|
P3
ILE
TYR159
LYS66
LEU156
GLU152
ASN70
TYR7
GLN114
GLU24
SER99
|
P4
ASN
LYS66
GLU152
ASN70
|
P5
PHE
PHE74
VAL97
GLU152
ASN70
GLN114
VAL9
GLU24
TYR116
TYR22
SER73
SER99
|
P6
GLU
ALA150
ASP77
ARG155
GLU152
TRP147
|
P7
LYS
LYS146
TRP147
SER73
ASP77
VAL76
|
P8
LEU
TYR123
THR80
LYS146
TYR84
TYR116
LEU81
TRP147
ASP77
ILE95
ILE124
THR143
|
Colour key
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]
A Pocket
TYR159
THR163
TRP167
TYR171
LEU5
TYR59
GLU63
LYS66
TYR7
|
B Pocket
GLU24
VAL34
TYR45
GLU63
LYS66
ALA67
TYR7
ASN70
VAL9
SER99
|
C Pocket
ASN70
SER73
PHE74
VAL9
VAL97
|
D Pocket
GLN114
ARG155
LEU156
TYR159
LEU160
SER99
|
E Pocket
GLN114
TRP147
GLU152
LEU156
VAL97
|
F Pocket
TYR116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
TYR84
ILE95
|
Colour key
Data provenance
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
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYW 70 80 90 100 110 120 ERETQKAKGNEQSFRVDLRTLLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDG 130 140 150 160 170 180 CDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYLEGTCVEWLRRYLKNGNATLL 190 200 210 220 230 240 RTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRW |
3. Natural Killer Cell Receptor Ly49c
Natural Killer Cell Receptor Ly49c
|
10 20 30 40 50 60
GVVYWFCYSTKCYYFIMNKTTWSGCKANCQHYSVPILKIEDEDELKFLQRHVIPENYWIG 70 80 90 100 110 LSYDKKKKEWAWIDNGPSKLDMKIRKMNFKSRGCVFLSKARIEDIDCNIPYYCICGKKLD |
4. Peptide
|
SIINFEKL
|
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
Components
Data license
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.