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5AD0

Gaga-BF2*021:01 binding "GHAEEYGADTL" at 2.84Å 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
Gaga-BF2*021:01
['A']
3. Peptide
GHAEEYGADTL
['C']

Species

Locus / Allele group

GAGA-BF2 / Gaga-BF2*021

Publication

Complex of a B21 Chicken Mhc Class I Molecule and a 11mer Chicken Peptide

Chappell, P.E., Roversi, P., Harrison, M.C., Kaufman, J.F., Lea, S.M.

Structure deposition and release

Deposited: 2015-08-19
Released: 2016-09-28
Revised: 2016-09-28

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication

Peptide details

Length: Undecamer (11 amino acids)

Sequence: GHAEEYGADTL

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 GLY

GLU62
TYR156
ARG61
LEU5
TYR58
TYR7
TRP164
PHE33
TYR168
 P10 THR

ASN76
TYR149
THR140
ILE72
TRP144
TRP95
 P11 LEU

ARG83
TRP95
VAL121
PHE120
LYS143
ASN76
VAL93
ALA113
ILE79
LEU80
THR140
 P2 HIS

ASP24
ILE65
ARG9
GLU62
VAL66
TYR156
ARG61
MET34
TYR7
 P3 ALA

ILE65
TYR156
 P4 GLU

ARG61
ILE65
 P5 GLU

TYR149
 P6 TYR

GLN64
GLY68
ILE65
ILE72
SER69
 P7 GLY

TYR149
ILE72
TRP144
 P8 ALA

HIS111
LEU153
TYR149
TRP144
TRP95
 P9 ASP

TRP144
TRP95
SER69
ASN73
HIS111
ASN76
ARG9
ILE72

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
DLTPKVQVYSRFPASAGTKNVLNCFAAGFHPPKISITLMKDGVPMEGAQYSDMSFNDDWT
        70        80        90
FQRLVHADFTPSSGSTYACKVEHETLKEPQVYKWDPEF
2. Class I alpha
Gaga-BF2*021:01
        10        20        30        40        50        60
MGSCGALGLGLLLAAVCGAAAELHTLRYIRTAMTDPGPGLPWFVDVGYVDGELFMHYNST
        70        80        90       100       110       120
ARRAVPRTEWIAANTDQQYWDRETQIVQGSEQINRENLDILRRRYNQTGGSHTVQWMSGC
       130       140       150       160       170       180
DILEDGTIRGYHQAAYDGRDFVAFDKGTMTLTAAVPEAVPTKRKWEEGGYAEGLKQYLEE
       190       200       210       220       230       240
TCVEWLRRYVEYGKAELGRRERPEVRVWGKEADGILTLSCRAHGFYPRPIVVSWLKDGAV
       250       260       270       280       290       300
RGQDAQSGGIVPNGDGTYHTWVTIDAQPGDGDKYQCRVEHASLPQPGLYSWRSGGGLNDI
       310       320
FEAQKIEWHENSSSVDKLAAALEHHHHHH
3. Peptide
GHAEEYGADTL

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. 5AD0 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5AD0 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5AD0 assembly 1  
Peptide only [cif]
  1. 5AD0 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5ad0

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.