1IM9

HLA-C*04:01 binding "QYDDAVYKL" with KIR NK receptor at 2.80Å 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 and kir

1. Beta 2 microglobulin

['B']

2. Class I alpha
HLA-C*04:01

['A']

3. Killer Ig-Like Receptors

['D']

4. Peptide
QYDDAVYKL

['C']

Species

Homo sapiens (Human)

Locus / Allele group

HLA-C / HLA-C*04

Publication

Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1-HLA-Cw4 complex.

Fan QR, Long EO, Wiley DC

Nat. Immunol. (2001) 2, 452-60 [doi:10.1038/87766] [pubmed:11323700]

This nationwide population-based cohort study aimed to investigate the impact of systemic anti-inflammatory treatment on the major adverse cardiovascular events (MACE) risk in patients with psoriasis from January 2006 to December 2018, using a database provided by the Korean National Health Insurance Service. Patients were grouped based on the following treatment modalities: biologics, phototherapy, methotrexate, cyclosporine, and mixed conventional systemic agents. Patients who had not received any systemic treatment were assigned to the control cohort. The incidence of MACE per 1000 person-year was 3.5, 9.3, 12.1, 28.4, 39.5, and 14.5 in the biologic, phototherapy, methotrexate, cyclosporine, mixed conventional systemic agents, and control cohorts, respectively. During the 36-month follow-up, the cumulative incidence of MACE in the phototherapy and biologic cohorts remained lower than that of other treatment modalities. Cyclosporine (hazard ratio (HR) = 2.11, 95% confidence interval (CI) = 1.64-2.71) and mixed conventional systemic agents (HR = 2.57, 95% CI = 2.05-3.22) treatments were associated with increased MACE risk. Methotrexate treatment was not associated with MACE. Our finding demonstrates that treatment modalities may affect cardiovascular comorbidities in patients with psoriasis. Thus, an appropriate combination of anti-psoriatic therapies should be considered to manage patients with high cardiovascular risk.IRB approval status: Waiver decision was obtained by the institutional review board, Konkuk University Hospital, Seoul, Republic of Korea (KUH1120107).

Structure deposition and release

Deposited: 2001-05-10

Released: 2001-05-30

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: QYDDAVYKL

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

PHE99

THR163

GLU63

PHE33

TRP167

TYR171

TYR159

TYR59

LYS66

TYR7

MET5

P2 TYR

ARG97

PHE22

GLN70

TYR67

TYR159

TYR7

PHE99

ALA24

LYS66

GLU63

P3 ASP

ARG97

TYR159

PHE99

LYS66

ARG156

P4 ASP

LYS66

ARG69

TYR159

GLN155

P5 ALA

ARG97

GLN70

ARG156

GLN155

P6 VAL

GLN70

ARG156

ARG69

ALA73

P7 TYR

GLN70

ALA73

ASN77

ASP74

TRP147

SER9

SER11

GLU152

PHE116

PHE22

ARG156

LEU95

ARG97

P8 LYS

TRP147

ASN77

P9 LEU

TRP147

TYR84

LEU81

LYS80

THR143

PHE116

ILE142

LYS146

TYR123

LEU95

ASN77

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

LYS67

ARG7

ARG70

PHE9

MET99

C Pocket

ARG70

GLN73

ALA74

PHE9

GLN97

D Pocket

TYR114

GLU155

GLN156

ALA159

TYR160

MET99

E Pocket

TYR114

LYS147

ARG152

GLN156

GLN97

F Pocket

GLN116

ASP123

ILE143

ARG146

LYS147

VAL77

ARG80

LYS81

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-C04:01 IPD-IMGT/HLA* [ipd-imgt:HLA34864]	10 20 30 40 50 60 MGSHSMRYFSTSVSWPGRGEPRFIAVGYVDDTQFVRFDSDAASPRGEPREPWVEQEGPEY 70 80 90 100 110 120 WDRETQKYKRQAQADRVNLRKLRGYYNQSEDGSHTLQRMFGCDLGPDGRLLRGYNQFAYD 130 140 150 160 170 180 GKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKETL 190 200 210 220 230 240 QRAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAGDG 250 260 270 TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWK

3. Killer Ig-Like Receptors Killer Ig-Like Receptors	10 20 30 40 50 60 MHEGVHRKPSLLAHPGPLVKSEETVILQCWSDVMFEHFLLHREGMFNDTLRLIGEHHDGV 70 80 90 100 110 120 SKANFSISRMTQDLAGTYRCYGSVTHSPYQVSAPSDPLDIVIIGLYEKPSLSAQPGPTVL 130 140 150 160 170 180 AGENVTLSCSSRSSYDMYHLSREGEAHERRLPAGPKVNGTFQADFPLGPATHGGTYRCFG 190 200 210 220 SFHDSPYEWSKSSDPLLVSVTGNPSNSWPSPTEPSSKTGNPRHLH

4. Peptide	QYDDAVYKL

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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Complete structures

Aligned structures [cif]

1IM9 assembly 1

Components

MHC Class I alpha chain [cif]

1IM9 assembly 1

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

1IM9 assembly 1

Peptide only [cif]

1IM9 assembly 1

Derived data

Data for this page [json]

https://api.histo.fyi/v1/structures/1im9

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.