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6VB3

HLA-B*15:01 binding "TVAASGHSY" at 2.00Å 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
HLA-B*15:01
['A']
3. Peptide
TVAASGHSY
['C']

Species

Locus / Allele group

HLA-B / HLA-B*15

Publication

HLA-B*15:01 complexed with a synthetic peptide

Schutte, R.J., Li, D., Ostrov, D.A.

Structure deposition and release

Deposited: 2019-12-18
Released: 2020-11-25
Revised: 2020-11-25

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: TVAASGHSY

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 THR

TYR171
PHE33
TYR159
TYR7
LEU163
ARG62
TYR59
GLU63
TYR99
TRP167
MET5
 P2 VAL

LEU163
GLU63
ILE66
MET45
TYR7
ARG62
TYR9
TYR159
TYR99
 P3 ALA

ARG62
ILE66
TRP156
TYR99
ASN70
TYR9
TYR159
 P4 ALA

ARG62
ILE66
 P5 SER

ASN70
ILE66
THR69
 P6 GLY

THR73
ASN70
GLU152
 P7 HIS

GLU152
LYS146
TRP147
THR73
ALA150
 P8 SER

THR143
LYS146
THR73
GLU76
SER77
ASN80
TRP147
 P9 TYR

GLN96
SER77
THR143
LEU95
LYS146
TYR74
TRP147
TYR84
ARG97
TYR123
ILE124
LEU81
ASN80
SER116

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

ALA159
GLY163
GLU167
ARG171
SER5
GLU59
ARG63
GLN66
ARG7
B Pocket

ILE24
PHE34
ARG45
ARG63
GLN66
ILE67
ARG7
THR70
PHE9
MET99
C Pocket

THR70
GLN73
THR74
PHE9
GLN97
D Pocket

HIS114
GLU155
GLN156
ALA159
TYR160
MET99
E Pocket

HIS114
LYS147
ARG152
GLN156
GLN97
F Pocket

GLN116
ASP123
ILE143
ARG146
LYS147
GLU77
ARG80
ASN81
GLY84
THR95

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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
        70        80        90
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
2. Class I alpha
HLA-B*15:01
IPD-IMGT/HLA
[ipd-imgt:HLA35228]
        10        20        30        40        50        60
MGSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRMAPRAPWIEQEGPEY
        70        80        90       100       110       120
WDRETQISKTNTQTYRESLRNLRGYYNQSEAGSHTLQRMYGCDVGPDGRLLRGHDQSAYD
       130       140       150       160       170       180
GKDYIALNEDLSSWTAADTAAQITQRKWEAAREAEQWRAYLEGLCVEWLRRYLENGKETL
       190       200       210       220       230       240
QRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDR
       250       260       270
TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
3. Peptide
TVAASGHSY

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. 6VB3 assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6VB3 assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6VB3 assembly 1  
Peptide only [cif]
  1. 6VB3 assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6vb3

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.