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6KYU

Anpl-UAA binding "LRKRQLTVL" at 1.50Å 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
['A']
3. Peptide
LRKRQLTVL
['C']

Species

Locus / Allele group

ANPL-UAA / Anpl-UAA

Publication

Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the duck pAnpl-UAA

Liu, Z.X., Zhang, N.Z.

Structure deposition and release

Deposited: 2019-09-20
Released: 2020-09-23
Revised: 2020-12-30

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: LRKRQLTVL

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 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

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
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

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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. 6KYU assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6KYU assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6KYU assembly 1  
Peptide only [cif]
  1. 6KYU assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6kyu

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.