6LF9: MHC class I antigen

Crystal structure of pSLA-1*1301 complex with dodecapeptide RVEDVTNTAEYW. Determined by X-ray diffraction at 2.5 Å resolution. Released 17 Mar 2021.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Sus scrofa, synthetic construct
Chains: 12
Atoms: 12,718
Mol. weight: 176.49 kDa
Released: 17 Mar 2021

Explore 6LF9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LF9 contains 54 α-helices and 117 β-strands across 8 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	8
β-strand	20-28	9	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	51-54	4
α-helix	57-85	29
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	140-150	11
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
α-helix	181-182	2
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	199-208	10	10
β-strand	209	1	9
β-strand	214-219	6	11
α-helix	225-227	3
β-strand	229-230	2	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-249	9	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	12
α-helix	6-7	2
β-strand	8-13	6	13
β-strand	23-32	10	13
β-strand	33	1	12
β-strand	37-43	7	14
β-strand	46-47	2	14
α-helix	48-49	2
β-strand	51-52	2	13
α-helix	53-55	3
β-strand	56-57	2	13
β-strand	63-71	9	13
β-strand	79-85	7	14
β-strand	92-95	4	14

Chain D: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	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	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	225	1	4
α-helix	226-227	2
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

Chains E, H and K: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	5
α-helix	6-7	2
β-strand	8-13	6	6
β-strand	23-32	10	6
β-strand	33	1	5
β-strand	38-43	6	7
β-strand	46-47	2	7
α-helix	48-49	2
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Chain G: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	15
β-strand	20-28	9	15
β-strand	31-37	7	15
β-strand	46-47	2	15
α-helix	51-54	4
α-helix	57-84	28
β-strand	94-103	10	15
β-strand	109-118	10	15
β-strand	121-126	6	15
β-strand	133-135	3	15
α-helix	140-150	11
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
β-strand	183	1	16
α-helix	184-185	2
β-strand	186-193	8	17
β-strand	199-208	10	17
β-strand	209	1	16
β-strand	214-219	6	18
β-strand	229-230	2	17
α-helix	231-233	3
β-strand	234-235	2	17
β-strand	241-249	9	17
α-helix	254-256	3
β-strand	257-262	6	18
β-strand	270-272	3	18

Chain J: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	22
β-strand	20-28	9	22
β-strand	31-37	7	22
β-strand	46-47	2	22
α-helix	51-54	4
α-helix	57-85	29
β-strand	94-103	10	22
β-strand	109-118	10	22
β-strand	121-126	6	22
β-strand	133-135	3	22
α-helix	140-149	10
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	181-182	2
β-strand	183	1	23
α-helix	184-185	2
β-strand	186-193	8	24
β-strand	199-208	10	24
β-strand	209	1	23
β-strand	214-218	5	25
β-strand	229-230	2	24
α-helix	231-233	3
β-strand	234-235	2	24
β-strand	241-249	9	24
α-helix	254-256	3
β-strand	258-262	5	25
β-strand	270-272	3	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, D, G, J	protein	273	Sus scrofa	B1PJU7 (AlphaFold model)
Beta-2-microglobulin	B, E, H, K	protein	97	Sus scrofa	Q07717 (AlphaFold model)
Arg-val-glu-asp-val-thr-asn-thr-ala-glu-tyr-trp	C, F, I, L	protein	12	synthetic construct	P16082

Sequence of entity 1 (A, D, G, J), FASTA

>6LF9_1 MHC class I antigen (chains A, D, G, J)
GPHSLSYFYTAVSRPDRGDSRFIAVGYVDDTQFVRFDNYAPNPRMEPRVPWIQQEGQDYW
DEETRKVKDNAQTYGVGLNTLRGYYNQSEAGSHTLQSMFGCYLGPDGLLLHGYRQDAYDG
ADYIALNEDLRSWTAADMAAQITKRKWEAANVAERRRSYLQGLCVESLRRYLEMGKDTLQ
RAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGT
FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLR

Sequence of entity 2 (B, E, H, K), FASTA

>6LF9_2 Beta-2-microglobulin (chains B, E, H, K)
ARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSF
YLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH

Sequence of entity 3 (C, F, I, L), FASTA

>6LF9_3 ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP (chains C, F, I, L)
RVEDVTNTAEYW

Primary citation

Peptidomes and Structures Illustrate How SLA-I Micropolymorphism Influences the Preference of Binding Peptide Length. Wei, X.H., Wang, S., Zhang, N.Z. et al. Front Immunol (2022). DOI 10.3389/fimmu.2022.820881

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
6KWN 2.4 Å, Crystal structure of pSLA-1*1301(F99Y) complex with S-OIV-derived epitope NSDTVGWSW

Browse structure collections

About this viewer

MolViewer shows 6LF9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.