6KWN: MHC class I antigen

Crystal structure of pSLA-1*1301(F99Y) complex with S-OIV-derived epitope NSDTVGWSW. Determined by X-ray diffraction at 2.4 Å resolution. Released 9 Sept 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Sus scrofa, Swine influenza virus
Chains: 3
Atoms: 3,197
Mol. weight: 44.25 kDa
Released: 9 Sept 2020

Explore 6KWN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KWN contains 14 α-helices and 29 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
α-helix	14	1
β-strand	20-28	9	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	4
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-195	10	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
α-helix	225-227	3
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
α-helix	3-4	2
β-strand	5-10	6	6
β-strand	20-29	10	6
β-strand	30	1	5
β-strand	35-40	6	7
β-strand	43-44	2	7
β-strand	48-49	2	6
α-helix	50-52	3
β-strand	53-54	2	6
β-strand	60-68	9	6
β-strand	76-81	6	7
β-strand	89-92	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	275	Sus scrofa	B1PJU7 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Sus scrofa	Q07717 (AlphaFold model)
peptide	C	protein	9	Swine influenza virus	Q9Q0U7

Sequence of entity 1 (A), FASTA

>6KWN_1 MHC class I antigen (chains A)
GPHSLSYFYTAVSRPDRGDSRFIAVGYVDDTQFVRFDNYAPNPRMEPRVPWIQQEGQDYW
DEETRKVKDNAQTYGVGLNTLRGYYNQSEAGSHTLQSMYGCYLGPDGLLLHGYRQDAYDG
ADYIALNEDLRSWTAADMAAQITKRKWEAANVAERRRSYLQGLCVESLRRYLEMGKDTLQ
RAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGT
FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD

Sequence of entity 2 (B), FASTA

>6KWN_2 Beta-2-microglobulin (chains B)
FVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDW
SFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

Sequence of entity 3 (C), FASTA

>6KWN_3 peptide (chains C)
NSDTVGWSW

Primary citation

Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism. Wei, X., Wang, S., Li, Z. et al. Front Immunol (2021) 12:592447-592447. DOI 10.3389/fimmu.2021.592447 · PubMed

Other PDB entries of the same protein (UniProt B1PJU7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KWO 1.8 Å, Crystal structure of pSLA-1*1301 complex with mutant epitope ESDTVGWSW
6LF9 2.5 Å, Crystal structure of pSLA-1*1301 complex with dodecapeptide RVEDVTNTAEYW

Browse structure collections

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