Anpl-UAA binding "LRKRQLTVL" at 1.50Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Anpl-UAA
LRKRQLTVL
Species
Locus / Allele group
Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the duck pAnpl-UAA
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
LEU
CYS162
TYR169
TYR58
TYR157
GLY165
TYR7
LEU5
GLN62
THR161
|
P2
ARG
GLY26
TYR36
THR43
TYR97
GLN62
ASP34
ILE65
TYR7
SER24
VAL25
HIS35
SER66
TYR157
|
P3
LYS
ARG153
TYR157
ASP150
TYR97
ILE65
TRP154
|
P4
ARG
ILE65
TRP154
GLU64
ARG61
ARG153
|
P5
GLN
TYR113
ILE72
ALA69
PHE73
TYR97
ILE65
TRP154
ASP9
LEU95
|
P6
LEU
ARG153
ILE72
ASP150
|
P7
THR
ILE72
TRP144
ARG111
ASP150
GLU147
|
P8
VAL
LEU75
ASP76
GLU147
LYS143
ILE72
TRP144
|
P9
LEU
PHE120
ARG83
THR140
LEU80
THR79
ASP76
LYS143
TRP93
TRP144
|
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]
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
GQAKAAPKVQVYSRHPATAGTENILNCYVEGFHPPKIDIALLKNGEPMKDVKYNDMSFGD 70 80 90 100 DWTFQRLVYAPFTPTKSDVYTCRVDHEAFTEPQSFRWEPDF |
2. Class I alpha
Anpl-UAA
|
10 20 30 40 50 60
EPHSLRYFDTGVSDPSPGVPRFVSVGYVDGHLIDHYDSETQRTEPRADWFAANTDQQYWD 70 80 90 100 110 120 RQTEISRGAEQIFRLDLETLRERYNQSRGSHTWQLMYGCDLLEDGSTRGFRQYGYEGRDF 130 140 150 160 170 180 VAFDKDTLTFTAADAGAQITKRKWEQEGTDAERWKFYLENTCIEGLRKYVSYGKDVLERR 190 200 210 220 230 240 ERPEVQVSGMEADKILTLSCRAHGFYPRPISISWLKDGMVQEQETKRGSTVPNSDGTYHI 250 260 270 WATIDVLPGERDKYQCRVEHASLPQPGLFSW |
3. Peptide
|
LRKRQLTVL
|
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.