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5GJY

Anpl-UAA*01 binding "MVMELIRMI" at 1.71Å 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']
2. Class I alpha
Anpl-UAA*01
['A']
3. Peptide
MVMELIRMI
['C']

Species

Locus / Allele group

ANPL-UAA / Anpl-UAA*01

Publication

Structural Definition Of Duck MHC Class I Explains the Resistance to Influenza A virus

Wu, Y., Xia, C.

Structure deposition and release

Deposited: 2016-07-02
Released: 2017-05-10
Revised: 2017-05-10

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: MVMELIRMI

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 MET

TYR159
TYR10
TYR61
GLU65
LEU8
TYR171
TRP167
ARG64
 P2 VAL

ASN72
THR68
TYR159
SER69
TYR10
MET46
HIS100
TYR12
GLU65
THR27
 P5 LEU

GLN155
TYR159
GLN113
TRP156
 P6 ILE

TYR12
TRP156
HIS100
ASN72
ILE75
PHE76
 P7 ARG

THR151
ASN79
ILE75
GLU149
VAL152
GLN155
TRP146
 P8 MET

LYS145
VAL78
ASN79
TRP146
ILE75
 P9 ILE

LYS145
ARG86
ASN79
THR82
TRP96
THR142
TRP146
ALA83
PHE122

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]

Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
MEFGQAKAAPKVQVYSRHPATAGTENILNCYVEGFHPPKIDIALLKNGEPMKDVKYNDMS
        70        80        90       100
FGDDWTFQRLVYAPFTPTKSDVYTCRVDHEAFTEPQSFRWEPDF
2. Class I alpha
Anpl-UAA*01
        10        20        30        40        50        60
MEFEPHSLRYFYTAVSDPSPGVPQFVTVGSVDGEVFVRYDSETRKMEPRVDWIVANVDQQ
        70        80        90       100       110       120
YWDRETETSRGNEQIFRVNLDTARERYNQSRGSHTWQCMHGCDLEDGSIRGFQQCGYDGK
       130       140       150       160       170       180
DFIALDKDTLTYTAADAAAQITKRKWEQEGTVAEQWKNYLENTCIEWLRKYVSYGKDVLE
       190       200       210       220       230       240
RRERPKVRVSGMESNKILTLSCRAHGFYPPPISISWLKDGVVQEQETKRGSTVPNSDGTY
       250       260       270
HAWATIDVLPGNRDKYQCRVEHASLPQPGLFSW
3. Peptide
MVMELIRMI

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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   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. 5GJY assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5GJY assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5GJY assembly 1  
Peptide only [cif]
  1. 5GJY assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5gjy

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.