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5Y91

Ctid-UAA106 binding "FANFCLMMI" at 1.90Å 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
Ctid-UAA106
['A']
3. Peptide
FANFCLMMI
['C']

Species

Locus / Allele group

CTID-UAA / Ctid-UAA106

Publication

Crystal structure of bony fish MHC class I complex at 1.9 Angstroms resolution.

Zhaosan, C., Nianzhi, Z., Chun, X.

Structure deposition and release

Deposited: 2017-08-22
Released: 2017-09-20
Revised: 2017-09-20

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: FANFCLMMI

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 PHE

TYR168
ARG61
TRP164
GLN62
LEU6
TYR8
VAL65
TYR156
TYR58
 P2 ALA

TYR97
TYR10
LEU66
TYR8
VAL65
TYR156
GLN62
 P3 ASN

GLN152
ASN153
VAL65
TYR156
TYR97
TYR10
TYR111
 P4 PHE

THR160
GLN152
VAL65
 P5 CYS

ASN153
TYR111
GLN152
 P6 LEU

GLY68
VAL72
PHE73
VAL65
ALA69
TYR10
 P7 MET

VAL72
SER76
LYS143
LEU147
VAL149
TRP144
 P8 MET

VAL72
SER76
LYS143
ILE79
ASP75
TRP144
 P9 ILE

VAL80
TRP93
ARG83
SER76
PHE120
THR140
LYS143
TRP144
ILE79

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
MRALVSFALFCVLYISVQGKVSSPKIQVYSHYPGEYGKENTLICYVSGFHPPDISIELLK
        70        80        90       100       110
NGEVIADAQQTDLAFEKGWQFHLTKSVSFKPEKSDEYSCSVRHMSKTKKIVWESNM
2. Class I alpha
Ctid-UAA106
        10        20        30        40        50        60
GTHSLKYVYTGVSRGIDFPEFTAVGMVDDGQFMYFDSNSMKAVPKTEWIRQNEGADYWDR
        70        80        90       100       110       120
QTQVLIGAHQVFKDSIQIVMERFNQSKGVHTWQNMYGCELNDDGTTQGFYQYAYDGEDFV
       130       140       150       160       170       180
SLDKNTLTWTAANPQAVITKHKWEALAVAEQNKGYLENTCIEWLKKYVAYGKDTLERKVS
       190       200       210       220       230       240
PQVSLLQKDPSSPVTCHATGFYPSGVTITWQKNGQDHDEDVDLGELLPNEDGSFQRMSTL
       250       260       270
NVGPDEWKNNRFSCVVEHQDKTIRKTEDDIITNFD
3. Peptide
FANFCLMMI

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

Data can be downloaded to your local machine from the links below.
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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. 5Y91 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 5Y91 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5Y91 assembly 1  
Peptide only [cif]
  1. 5Y91 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5y91

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.