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5GJX

Anpl-UAA*01 binding "RLIQNSITI" at 2.06Å 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
RLIQNSITI
['C']

Species

Locus / Allele group

ANPL-UAA / Anpl-UAA*01

Publication

Structural Definition Of Duck MHC Class I For 2.06 Angstrom Explains its 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: RLIQNSITI

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 ARG

LEU8
TYR171
TYR61
TYR159
THR163
TRP167
GLU65
TYR10
 P2 LEU

TYR10
ASN72
MET46
TYR12
SER69
TYR159
HIS100
GLU65
THR27
THR68
 P3 ILE

HIS100
GLN155
THR68
TRP156
TYR159
ASN72
TYR12
 P4 GLN

ARG64
THR68
 P5 ASN

GLN155
 P6 SER

ASN72
ILE75
 P7 ILE

TRP146
GLU149
VAL152
ILE75
LYS145
ASN79
 P8 THR

VAL78
ILE75
LYS145
ASN79
TRP146
 P9 ILE

ASN79
TRP146
ALA83
ILE141
PHE122
TRP96
THR82
ARG86
LYS145
THR142

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
RLIQNSITI

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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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. 5GJX assembly 1  

Components

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

Derived data

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

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.