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5IND

HLA-B*58:11 binding "QASQDVKNW" at 2.13Å 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', 'D']
2. Class I alpha
HLA-B*58:11
['A', 'C']
3. Peptide
QASQDVKNW
['E', 'F']

Species

Locus / Allele group

HLA-B / HLA-B*58

Publication

Crystal structure of HLA-B*5801, a protective HLA allele for HIV-1 infection.

Li X, Lamothe PA, Ng R, Xu S, Teng M, Walker BD, Wang JH
Protein Cell (2016) [doi:10.1007/s13238-016-0309-y]  [pubmed:27638468] 

Structure deposition and release

Deposited: 2016-03-07
Released: 2016-10-05
Revised: 2016-10-19

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: QASQDVKNW

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 GLN

TYR59
GLU63
TRP167
LEU163
PHE33
TYR159
TYR7
MET5
TYR171
 P2 ALA

ASN66
TYR7
TYR9
TYR99
GLU63
MET67
TYR159
 P3 SER

TYR159
SER70
TYR99
ASN66
LEU156
TYR9
ARG97
MET67
 P4 GLN

ASN66
LEU156
 P5 ASP

SER70
TYR74
ASN66
TYR9
THR73
ARG97
 P6 VAL

VAL152
LEU156
GLN155
 P7 LYS

VAL152
ALA150
ASN77
THR73
TRP147
 P8 ASN

ILE80
LYS146
ASN77
THR143
GLU76
THR73
TRP147
 P9 TRP

TYR74
TYR118
ALA117
TYR84
TYR123
ILE142
LYS146
ASN77
ILE80
TRP147
THR143
SER116
ALA81
ILE95

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]

Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
A Pocket

TYR159
LEU163
TRP167
TYR171
MET5
TYR59
GLU63
ASN66
TYR7
B Pocket

ALA24
VAL34
THR45
GLU63
ASN66
MET67
TYR7
SER70
TYR9
TYR99
C Pocket

SER70
THR73
TYR74
TYR9
ARG97
D Pocket

ASP114
GLN155
LEU156
TYR159
LEU160
TYR99
E Pocket

ASP114
TRP147
VAL152
LEU156
ARG97
F Pocket

SER116
TYR123
THR143
LYS146
TRP147
ASN77
ILE80
ALA81
TYR84
ILE95

Colour key

Binds N-terminus Binds P1 backbone Binds P2 backbone Binds PC-1 backbone Binds C-terminus

Data provenance

N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.

Chain sequences

1. Beta 2 microglobulin
Beta 2 microglobulin
        10        20        30        40        50        60
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
        70        80        90
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. Class I alpha
HLA-B*58:11
IPD-IMGT/HLA
[ipd-imgt:HLA02201]
        10        20        30        40        50        60
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DGETRNMKASAQTYRENLRIALRYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
       130       140       150       160       170       180
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
       190       200       210       220       230       240
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPH
3. Peptide
QASQDVKNW

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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   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. 5IND assembly 1  
  2. 5IND assembly 2  

Components

MHC Class I alpha chain [cif]
  1. 5IND assembly 1  
  2. 5IND assembly 2  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5IND assembly 1  
  2. 5IND assembly 2  
Peptide only [cif]
  1. 5IND assembly 1  
  2. 5IND assembly 2  

Derived data

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

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.