1VGK

H2-Kd binding "SYVNTNMGL" at 2.06Å 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.

Complex type

Class i with peptide

1. Beta 2 microglobulin

['B']

2. Class I alpha
H2-Kd

['A']

3. Peptide
SYVNTNMGL

['C']

Species

Mus musculus (Mouse)

Locus / Allele group

H2-K / H2-Kd

Publication

The crystal structure of class I major histocompatibility complex, H-2Kd at 2.0 A resolution

Zhou, M., Xu, Y., Liu, Y., Gao, G.F., Tien, P., Rao, Z.

Structure deposition and release

Deposited: 2004-04-27

Released: 2005-06-28

Revised: 2011-07-13

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: SYVNTNMGL

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 SER

TYR171

PHE99

ARG66

TRP167

GLU163

GLN63

LEU5

TYR159

TYR59

TYR7

PHE33

P2 TYR

TYR7

VAL9

ALA24

PHE22

ASP70

PHE99

PHE74

PHE45

ARG97

GLU163

ARG66

GLN63

ALA67

TYR159

P3 VAL

ASP70

TYR155

ARG97

ARG66

TYR156

TYR159

PHE99

P4 ASN

GLN65

TYR156

ALA67

SER69

ASP70

TYR155

ARG97

ARG66

P5 THR

ASP70

TYR155

ARG97

TYR156

TRP147

TRP73

PHE116

GLN114

P6 ASN

TRP73

ASP152

TYR155

TYR156

P7 MET

TRP147

LYS146

TRP73

ALA150

ASP152

TYR156

P8 GLY

TRP147

LYS146

TRP73

THR143

P9 LEU

LYS146

ALA81

TYR123

TRP147

THR80

TRP73

PHE95

SER77

TYR84

THR143

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

GLU163

TRP167

TYR171

LEU5

TYR59

GLN63

ARG66

TYR7

B Pocket

ALA24

VAL34

PHE45

GLN63

ARG66

ALA67

TYR7

ASP70

VAL9

PHE99

C Pocket

ASP70

TRP73

PHE74

VAL9

ARG97

D Pocket

GLN114

TYR155

TYR156

TYR159

LEU160

PHE99

E Pocket

GLN114

TRP147

ASP152

TYR156

ARG97

F Pocket

PHE116

TYR123

THR143

LYS146

TRP147

SER77

THR80

ALA81

TYR84

PHE95

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 H2-Kd	10 20 30 40 50 60 GPHSLRYFVTAVSRPGLGEPRFIAVGYVDDTQFVRFDSDADNPRFEPRAPWMEQEGPEYW 70 80 90 100 110 120 EEQTQRAKSDEQWFRVSLRTAQRYYNQSKGGSHTFQRMFGCDVGSDWRLLRGYQQFAYDG 130 140 150 160 170 180 RDYIALNEDLKTWTAADTAALITRRKWEQAGDAEYYRAYLEGECVEWLRRYLELGNETLL 190 200 210 220 230 240 RTDSPKAHVTYHPRSQVDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGT 250 260 270 FQKWAAVVVPLGKEQNYTCHVHHKGLPEPLTLRW

3. Peptide	SYVNTNMGL

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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This can then be used to load the structure/data directly from the url into an application like PyMol (for 3D structures) using the load command:

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]

1VGK assembly 1

Components

MHC Class I alpha chain [cif]

1VGK assembly 1

MHC Class I antigen binding domain (alpha1/alpha2) [cif]

1VGK assembly 1

Peptide only [cif]

1VGK assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/1vgk

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

Protein Data Bank Europe - Coordinate Server
1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
PyMol - PyMol.org/pymol
Levenshtein distance - Wikipedia entry
Protein Data Bank Europe REST API - Molecules endpoint
3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
Protein Data Bank Europe REST API - Publication endpoint
PubMed Central Europe REST API - Articles endpoint

This work is licensed under a Creative Commons Attribution 4.0 International License.