HLA-B*07:02 binding "EPRSPSHSM" at 2.10Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
HLA-B*07:02
EPRSPSHSM
Species
Locus / Allele group
CRYSTAL STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH PHOSPHOPEPTIDE NEOANTIGENS
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
GLU
GLU163
TRP167
TYR171
PHE33
MET5
ARG62
TYR7
TYR159
TYR59
ASN63
|
P2
PRO
GLU45
TYR159
TYR9
ASN63
ILE66
TYR67
TYR99
TYR7
ARG62
|
P3
ARG
ARG62
TYR116
GLN155
GLN70
TYR159
ILE66
ASP114
TYR9
ARG156
TYR99
|
P5
PRO
THR73
ILE66
ALA69
GLN155
GLN70
|
P6
SER
ARG156
GLN155
THR73
GLU152
GLN70
|
P7
HIS
GLU152
ALA150
TRP147
LYS146
ARG156
SER77
THR73
|
P8
SER
LYS146
SER77
ASN80
THR73
GLU76
TRP147
|
P9
MET
ILE124
TRP147
TYR84
TYR123
LYS146
THR143
LEU81
ASN80
TYR116
LEU95
SER77
|
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
GLU163
TRP167
TYR171
MET5
TYR59
ASN63
ILE66
TYR7
|
B Pocket
SER24
VAL34
GLU45
ASN63
ILE66
TYR67
TYR7
GLN70
TYR9
TYR99
|
C Pocket
GLN70
THR73
ASP74
TYR9
SER97
|
D Pocket
ASP114
GLN155
ARG156
TYR159
LEU160
TYR99
|
E Pocket
ASP114
TRP147
GLU152
ARG156
SER97
|
F Pocket
TYR116
TYR123
THR143
LYS146
TRP147
SER77
ASN80
LEU81
TYR84
LEU95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
2. Class I alpha
HLA-B*07:02
IPD-IMGT/HLA
[ipd-imgt:HLA34746] |
10 20 30 40 50 60
GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYW 70 80 90 100 110 120 DRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHDQYAYDG 130 140 150 160 170 180 KDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGECVEWLRRYLENGKDKLE 190 200 210 220 230 240 RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT 250 260 270 FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE |
3. Peptide
|
EPRSPSHSM
|
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.